Dissertations / Theses on the topic 'Residue conservation'

Conservation tillage production systems for flue-cured tobacco (Nicotiana tabacum L.) have been studied for many years. Inadequate chemical weed control and lack of acceptable pesticide and fertilizer application resulted in consistently lower yields and inferior cured leaf quality. The development of new conservation tillage equipment, improved methods of fertilizer application, and new herbicides, have resulted in a renewed interest in conservation tillage labeled for tobacco. This research investigated management practices to address slow early season growth characteristic of strip-tillage tobacco production. Objectives of the first study were to evaluate the methods of starter fertilizer application and determine the optimal rate. A transplant water treatment (11 kg ha-1) and 3 rates (11, 22, and 45 kg ha-1) of injected 9-45-15 (N:P2O5:K2O) water soluble starter fertilizer were evaluated for early season plant growth and time of topping. Starter fertilizer treatments increased tobacco root weight by 22% and leaf area up to 41%. Earlier topping was observed as a result of starter fertilizer with 23 and 6% more plants topped during the initial topping date in 1999 and 2000, respectively. Starter fertilizer did not consistently increase the yield of either strip-tillage or conventional tillage tobacco. The objectives of the second study were to compare the use of raised beds with flat-planting and investigate cover crop residue management techniques. Residue management treatments minimized residue within the strip-tilled area with an early hooded spray application (strip-killed) of a burndown herbicide as opposed to the traditional broadcast burndown application. The use of raised beds for strip-tillage production of tobacco showed no clear benefit when compared to flat-planting. Strip-tillage plots were similar to conventional tillage for cured leaf quality and yield. Early season strip-kill burndown herbicide applications proved beneficial in reducing difficulties incorporating residue into the strip-tilled area thus improving the quality of the prepared seed bed. This research has added to the present knowledge regarding strip-tillage tobacco production, and refined necessary cultural practices. Transplant starter fertilizer is recommended to overcome the typical slow early season growth characteristic of strip-tilled tobacco. However, increased rates (greater than 11 kg ha-1) or under-row injection of the material had no added benefit. The research also demonstrated that the use of raised beds should not be considered a necessary practice with the use of a strip-till implement that incorporates under-row subsoil tillage. This research has demonstrated that tobacco yields and quality comparable to conventional tillage can be realized using strip-tillage production techniques.
Master of Science

Thesis (MSc)--Stellenbosch University, 2015.
ENGLISH ABSTRACT: Annual medic pastures play an important role in conservation agriculture (CA) practices in the Western Cape, because of the beneficial role it plays in rotation systems and the fact that it can re-establish on its own. In the Overberg medic pastures are the main pasture short rotation crop, but farmers in recent years shifted away from including medics. This was due to unsuccessful re-establishment and a visible decrease in dry matter production. This trend started after CA practices were implemented for a few years. A field study conducted during 2013 investigated medic re-establishment and production following a wheat, barley, oat and medic pasture production year ( WM, BM, OM and MM) of which residues were left on the soil surface at different cover percentage levels (100%, 75%, 50%, 25% and 0%). The objective of this study was to determine what the effect of different amounts of residues was on annual medic re-establishment and production. Data from this study suggest that management of annual medic pastures should aim to re-sow the medic pasture if plant count drops below 78 pants per square meter. Weed management is of cardinal importance as it competes for resources, light and space and decrease medic pasture re-establishment and production. The data also indicates that the wheat/medic sequence is the best option when applying a short cash crop/annual pasture cropping system. Producers should manage their animals to ensure that a 50% to 75% cover is left on top of the soil following the grazing of residues during the summer months. The study in 2013 should have been replicated, but due to the low levels of re-establishment and production a decision was made to re-plant the trial sites. The field study conducted during 2014 investigated the medic/clover establishment and production following a re-plant. Medics were replanted following a W, B, O and M season, respectively. Residues again were manipulated to different cover percentages (100%, 75%, 50%, 25% and 0%). The objective was again to look at the amount and type of residues on medic/clover establishment and production following re-plant. Data from this study indicated that it might be advisable for annual medic/clovers to be re-sown after a cereal production year rather than a medic pasture year. With the production of medic/clover pastures not being affected by the residue cover percentage, a 100% residue cover following re-plant is best in rotations, if the optimal effect of CA wants to be observed. If animals are included in the production cycle, grazing of residues during summer months can occur until 50% cover is left. Soils will take longer to reach its potential, but by including animals the gross margin is more stable year on year. Two supplementary studies were conducted to investigate the germination of annual medics under controlled conditions. The objectives of the first supplementary study was to investigate the physical barrier effect of residues at different percentage cover (100%, 75%, 50%, 25% and 0%) and a possible allelopathic action from different types of residues (wheat, barley, oat and medic) on the annual medic cultivar Cavalier (one of the cultivars used during 2014 field re-plant). The different amounts of residue had no significant effect on percentage emergence of Cavalier. The 0% residue cover having the slightly higher germination could be because there are no physical obstructions preventing seedlings to establish. The different types of residue cover had no significant effect on the germination of annual medics, as the germination under wheat, barley, oats and medic residues did not differ from the control. The control had a slightly higher germination percentage (85%), while germination under residues was just below the recommended germination rate of 80-85%. This could be an indication of allelopathy from residues. The objective of the second supplementary study was to investigate the allelopathic effects of different residue leachates (wheat, barley, oat and medic) at different levels of concentrations (100% leachate, 75%, 50%, 25% and distilled water being the control) on Cavalier germination. The interaction between leachate type and concentration were significant. Low levels of leachate concentration did not have a significant impact on medic germination when compared between each other and the control. When the concentration percentage was increased differences were detected. Cavalier germination decreased drastically when medic leachate concentration increased, indicating allelopathic effects. Cavalier germination followed the same trend, just not as drastic, when wheat leachate concentration increased. This indicates that wheat could also have a negative allelopathic effect. With oat leachate Cavalier germination did not decrease except when 100% concentrate was used, which could indicate a small allelopathic effect. Cavalier germination following barley leachate showed no effect as concentration increased, even showing the odd increase. Depending on repeatability or follow-up studies of these experiments, data suggest that re-plant of medic pastures is beneficial if plant count drops below sustainable levels. Management of weeds during the medic pasture year improves production. Annual medic pastures should be re-planted following a cereal production year rather than a previous pasture year. Thus single medic rotations are preferred, for example WMWM rotation. Greater amounts of residues are beneficial for CA effects, but allelopathic effects of wheat and oat residues should be taken in consideration during re-establishment and residue levels should be lowered.
AFRIKAANSE OPSOMMING: Eenjarige medic weidings speel ʼn belangrike rol in bewaring landbou (CA) praktyke in die Wes Kaap, vanweë sy vermoë om jaarliks op sy eie te hervestig en sy voordelige rol in rotasie stelsels. Eenjarige medic weidings is tans die hoof kort rotasie gewas in die Overberg, maar boere is tans besig om dit uit die rotasie uit te sluit. Dit is as gevolg van lae hervestiging sowel as die opvallende afname in produksie. Hierdie waarnemings het na ʼn paar jaar na die toepassing van CA praktyke begin. Gedurende 2013 is daar ʼn veldstudie voltooi rakende medic weiding hervestiging en produksie wat na ʼn koring, gars, hawer en medic weiding produksie jaar volg (WM, BM, OM en MM). Gedurende die studie is stoppels by verskillende persentasie vlakke van bedekking op die grond gelaat (100%, 75%, 50%, 25% en 0% bedekking). Die doel van die studie was om die invloed van verskillende tipes en hoeveelhede stoppels op die hervestiging en produksie van eenjarige medic weidings vas te stel. Data van hierdie studie dui aan dat jaarlikse medic weidings so bestuur moet word dat medics in die Overberg area se plant telling nie laer as 78 plante per vierkante meter daal nie. Onkruid bestuur is van kardinale belang, omdat dit kompeteer met medics en veroorsaak ʼn verlaging in hervestiging en opbrengs. Data dui ook aan dat ʼn koring/medic stelsel die beste opsie is wanneer ʼn kort kontant gewas/eenjarige weiding gewas stelsel toegepas word. Produsente moet hul vee so bestuur dat ʼn 50 tot 75% stoppel bedekking gedurende die somer maande oorgelaat word na beweiding. Die herhaling van die 2013 veld studie was van plan, maar ag gevolg van lae hervestiging en produksie was die proef kampe oor geplant. Die veldstudie in 2014 was medic/klawer vestiging en produksie na herplanting ondersoek. Die medic/klawer saad is geplant na ʼn koring, gars, hawer en medic weiding seisoen onderskeidelik. Stoppels is weereens na verskillende bedekking persentasies verander (100%, 75%, 50%, 25% en 0% bedekking). Die doel was om te kyk wat die effek van verskillende tipes en hoeveelhede stoppels op eenjarige medic/klawer weiding is na herplant. Data wys dat medic/klawer weidings verkieslik herplant moet word na ʼn graan produksie jaar as ʼn medic weiding produksie jaar. Die medic/klawer weiding is nie geaffekteer deur die hoeveelheid stoppels op die grond oppervlakte nie, dus is ʼn 100% stoppel bedekking verkieslik vir optimale CA effekte. As diere in die sisteem teenwoordig is, kan stoppels bewei word gedurende die somer maande tot ʼn 50% bedekking bereik word. Grond sal langer vat om sy potensiaal te bereik, maar die jaarlikse bruto marge sal meer stabiel wees. Twee aanvullende studies is onderneem en ontkieming van eenjarige medics is ondersoek onder beheerde toestande. Die doelwit van die eerste aanvullende studie was om te kyk na die fisiese versperring effek van stoppels by verskillende persentasie bedekking (100%, 75%, 50%, 25% en 0%) en ʼn moontlike allelopatiese effek van verskillende tipe stoppels (koring, gars, hawer en medic) op die eenjarige medic kultivar Cavalier. Verskillende hoeveelhede stoppels het geen beduidende uitwerking op die vestiging van Cavalier gehad nie. Die 0% stoppel bedekking het ʼn effens hoër vestiging gehad. Dit kon wees as gevolg van geen fisiese versperring wat die saailing verhoed om te vestig nie. Die verskillende tipes stoppels het geen beduidende uitwerking op die ontkieming van eenjarige medics nie, die vestiging onder koring, gars, hawer en medic stoppels het nie statisties verskil van die kontrole nie. Die kontrole het wel ʼn effense hoër persentasie vestiging gehad (85%), terwyl die vestiging onder die stoppels onder die aanbevole koers van 80-85% was. Dit kan dalk ʼn allelopatiese effek van die stoppels aandui. Die doel van die tweede aanvullende studie was om die allelopatiese effek van die verskillende tipes stoppels (koring, gars, hawer en medic) by verskillende vlakke van konsentrasie (100%, 75%, 50%, 25% van die onverdunde loogsel en gedistilleerde water as kontrole) op Cavalier ontkieming. Daar was ʼn beduidende interaksie tussen tipe en konsentrasie loogsel. Met lae konsentrasie vlakke van loogsel was daar nie ʼn werklike impak op Cavalier ontkieming tussen die verkillende tipes en die kontrole nie. Slegs wanneer die konsentrasie persentasie verhoog is, is verskille waargeneem. Cavalier ontkieming het drasties af geneem soos die medic loogsel konsentrasie toegeneem het, wat ʼn negatiewe allelopatiese en verhoogde osmolaliteit effek wys. Cavalier ontkieming het dieselfde tendens gewys wanneer koring loogsel konsentrasie verhoog was, maar nie so drasties soos medic loogsel. Dit dui daarop dat koring ook ʼn negatiewe allelopatiese effek wys. Met hawer loogsel het Cavalier ontkieming slegs by die 100% konsentrasie pyl afgeneem, wat op ʼn lae allelopatiese effek dui. Cavalier ontkieming onder gars loogsel het geen verandering gewys as konsentrasies toegeneem het nie, en het selfs ʼn toename in ontkieming in party gevalle ondergaan. Afhangend van herhaling of op-volg studies van hierdie eksperimente, wys die data dat dit voordelig is om medic weidings te herplant as plant telling onder 78 plante per vierkante meter daal. Die bestuur van onkruid tydens die medic weidings jaar verbeter opbrengs. Eenjarige medic weidings moet herplant word na ʼn graan produksie jaar liewer as ʼn vorige weidings jaar. Medics moet dus in ʼn eenjarige rotasie stelsel wees, byvoorbeeld WMWM rotasie. Meer stoppels is voordelig vir CA promosie, maar allelopatiese stowwe van koring en hawer stoppels moet in ag geneem word en stoppels moet verlaag word vir hervestiging.

Tillage practices have changed dramatically during the past several decades as agricultural specialists have recognized the unfavorable environmental effects of mechanized tillage. Alternatively, conservation tillage management can mitigate adverse environmental impacts of tillage, such as soil and water degradation. Adoption of conservation tillage has continued to increase since its first introduction, which raises questions of when and where it is practiced. Spatial and temporal specifics of tillage practices form important dimensions for development of effective crop management practices and policies.  Because Landsat has been and will continue to image the Earth globally, it provides opportunities for systematic mapping of crop residue cover (CRC) /tillage practices. Thus, the overall objective of this study is to develop methodologies to improve our ability to monitor crop management across different landscapes in a time-efficient and cost-effective manner using Landsat TM and ETM+ imagery, which is addressed in three separate studies. The first study found that previous efforts to estimate CRC along a continuum using Landsat-based tillage indices were unsuccessful because they neglected the key temporal changes in agricultural surfaces caused by tilling, planting, and crop emergence at the start of the growing season. The first study addressed this difficulty by extracting minimum values of multi-temporal NDTI (Normalized Difference Tillage Index) spectral profiles, designated here as the minNDTI method. The minNDTI improves crop residue estimation along a continuum (R2 = 0.87) as well as tillage classification accuracy (overall accuracy > 90%).   A second study evaluated effectiveness of the minNDTI approach for assessing CRC at multiple locations over several years, and compared minNDTI to hyperspectral tillage index (CAI), and the ASTER tillage index (SINDRI). The minNDTI is effective across four different locations (R2 of 0.56 ~ 0.93). The third study, built upon the second study, addressed the Landsat ETM+ missing data issue, and devised methodologies for producing field-level tillage data at broad scales (multiple counties).  In summary, this research demonstrates that the minNDTI technique is currently the best alternative for monitoring CRC and tillage practices from space, and provides a foundation for monitoring crop residue cover at broad spatial and temporal scales.
Ph. D.

A two year study was initiated in 2001 on a 2.4 ha site of mostly St. Amable loamy sand and shallow loamy sand at the Macdonald Campus Research Farm. This study sought to assess the effects of long term tillage and residue practices on soil physical properties and to relate these properties to their influence on total carbon, total nitrogen and soil microbial biomass-carbon. The site was set up as a factorial experiment with three tillage practices (no till---NT; reduced till---RT; and conventional till---CT) and two residue practices (with residue (grain corn), +R; without residue (silage corn), -R). Soil physical properties measured were bulk density, macroporosity at -6 kPa, saturated hydraulic conductivity (Ksat ), dry aggregate distribution, soil moisture and soil temperature. Wheel versus non-wheel track bulk density was also determined in the NT plots. Total porosity, soil water characteristic curves and pore volume distribution were derived from field samples. Crop yield was also assessed. Tillage alone had an effect on total porosity, bulk density, pore diameter and macroporosity. No individual physical property was significantly affected by the residue treatments; however, the tillage and residue interaction was significant for Ksat, soil moisture and soil temperature. Dry aggregate distribution was not affected by either tillage, residue or the combination of the two. Tillage affected total carbon and total nitrogen in the 0--0.10 m depth. Soil microbial biomass-carbon was affected by residue inputs. Total carbon and nitrogen were influenced by the bulk density, but none of the other soil physical properties. Soil microbial biomass-carbon was not influenced by any of the physical properties. Tillage and residue practices had no significant effect on crop yield for either year.

Decomposition and N dynamics of grain-corn residues were investigated in a field study in southwestern Quebec, with particular reference to the roles of different plant parts (stems, leaves etc.) in determining overall residue mass loss and N content. A litterbag study was conducted, with surface and buried placements in plots under three tillage systems (no-till, reduced tillage, and conventional tillage, established five years before litterbag placement). Residue mass loss and N content were monitored over a two-year period. Separate data were obtained for leaves, stems, husks, and cobs. Net values for all residues combined were calculated taking into account initial proportions of each plant part at harvest. Overall estimates were made based on residue depth-distribution typical of each tillage system. A spreadsheet-based model of surface residue mass loss was developed, incorporating litterbag mass and other surface-residue data, in order to determine how well litterbag results predicted surface residue mass loss in the field, and to test alternative assumptions regarding residue decomposition and/or burial. Buried residues lost mass more quickly than surface residues, as expected. Thus residue breakdown would be fastest in a conventional system, slowest under no-till, and intermediate with reduced tillage. Substantial decreases in mass and residue N content occurred between fall placement and first sampling in spring, despite low temperatures for much of this period. Mass loss in the first period was substantial for stems as we as husks and leaves. Cobs decomposed most slowly throughout. Nitrogen dynamics, including effects of depth on residue N content, differed greatly by residue type. All the lower-N residues (cobs, husks, stems) immobilized N at some point. However, during the two-year study, N immobilization by one or more residue types was always counterbalanced or exceeded by N release by other residue, at least for the sampling intervals included. Pa

Much of Haitian agriculture is characterized by subsistence farming systems on eroded and nutrient-poor soils. Implementation of Conservation Agriculture systems has proven effective at improving soil quality and crop yield in many areas of the world, including areas similar to those in Haiti. While most Haitian smallholder farmers are highly resource-limited and adoption of new technologies is limited, these farmers are known to adopt new crops and practices if benefits that outweigh risks are demonstrated. Cover crops that help provide soil cover and increase nutrient mineralization are one of the most potentially beneficial changes that could be made on most smallholder farms. However, before specific cover crop recommendations can be made, their potential benefits need to be quantified. One field experiment in the summer of 2013 assessed decomposition rates and nutrient mineralization from common cash crops and two potential cover crops either on the soil surface or buried at 15 cm. The relative difficulty and expense of conducting these types of field trials led to the development and assessment of a laboratory-based system that could be used to simulate plant residue decomposition and nutrient release under controlled conditions. Additional benefits of a laboratory-based study include the ability to test significantly more treatment combinations than would likely be possible under field conditions and to control nearly all other experimental variables, other than the desired treatment comparisons.
Master of Science

High-biomass cover cropping enhances marketable yields in organic production of vegetables, linked to the improvement of soil quality and weed control. Although, during transition from chemical to organic cover-cropping production, especially with no-till systems, reduction of nitrogen availability to the main crop and increase in weed and pest pressure may occur. In 2004-2005, summer and fall broccoli (Brassica oleraceae L. Botrytis Group) crops were grown in twin rows on permanent (controlled traffic) raised beds (185-cm wide). Before broccoli transplanting, high-biomass cover crops were grown in specific bed areas. Legumes (Vicia villosa, Glycine max L., and Crotolaria juncea L.) on bed tops (grow zones) and grass species (Secale Cereale L., Setaria italica L., and Sorghum bicolor X S. bicolor var. Sudanese) in the alleyways (bed shoulders and bottoms). Experimental treatments were tillage (conventional, CT; and no-tillage, NT), farmscaping (with and without), and nitrogen sidedressing (with and without, applied 3 weeks after transplanting as a mixture of sodium nitrate - 22 kg N ha-1 - and feathermeal - 44 kg N ha-1). Weeds were managed by mechanical cultivation in CT and a spot weeding by hand in NT treatments. High numbers of beneficial insects (Cotesia glomerata, Cotesia orobenae and Diadegma insulare) kept the primary insect pest population (Pieris rapae, Evergestis rimosalis (Guenee), and Plutella xylostella) at a pest to predator ratio below 4:1. Although the excellent insect pest control was attributed to the farmscape plantings, pest level and crop yields were not significantly affected by farmscaping (likely due to the close proximity of the farmscaped plots (10-50m from non-farmscaped)). Broccoli yield averaged 62% higher in fall than summer (12.1 vs. 7.5 t ha-1) likely due to cool weather conditions during broccoli head development (October), increasing head size, uniformity, and marketability. In 2004, broccoli yield in CT plots was either equal or slightly higher than NT (9.5 vs. 9.0 t ha-1). However, in 2005, broccoli yield in CT plots was significantly higher in both spring (8.8 vs. 6.8 t ha-1; p = 0.0258) and fall crops (13.5 vs. 12.3 t ha-1 with p = 0.0484). Nitrogen sidedressing improved yield in all plots (9.8. vs. 12.7 t ha-1) and particularly in NT (8.6 vs. 12.1 t ha-1), indicating that availability and/or synchrony of nitrogen was a limiting factor. Incorporating high-N legume residues in the grow zones resulted in a lesser N response in CT.
Master of Science

The impact of tillage and residue management on soil microorganisms was studied over the maize (Zea mays L.) growing season in southwestern Quebec. Tillage and residue treatments were imposed on a sandy loam to loamy sand soil in fall 1991. Treatments consisted of no till, reduced tillage, and conventional tillage with crop residues either removed from (-R) or retained on (+R) experimental plots, laid out in a randomized complete block design. Soil microbial biomass carbon (SMB-C), soil microbial nitrogen (SMB-N) and phospholipid fatty acid (PLFA) concentrations were measured four times, at two depths (0--10 cm, 10--20 cm), over the 2001 growing season. Sample periods were: May 7th (pre planting), June 25 th, July 16th, and September 29th (prior to corn harvest). The effect of time was of a greater magnitude than those attributed to tillage or residue treatments. While SMB-C showed no seasonal change (160 mug C g-1 soil); SMB-N was responsive to mineral nitrogen fertilizer; and PLFA data showed an increase in fungi and total PLFA throughout the season. PLFA profiles showed better distinction between sampling period, and depth, than treatments. Of the two treatments, the effect of residue was more pronounced than that of tillage, with increased SMB-C and SMB-N (6.1% and 96%) in +R plots compared to -R plots. This study illustrated that measuring soil quality based on soil microbial components must take into account seasonal changes in soil physical, chemical conditions, and nutrient supply.

The reported requirement for a higher weeding effort due to increased weed infestations under conservation agriculture (CA) relative to conventional mouldboard plough tillage is perceived by both smallholder farmers and extension workers as the main limiting factor to the widespread adoption of CA by smallholder farmers in southern Africa. However, proponents of CA argue that weeds are only a problem under CA in the initial two years and decline afterwards resulting in reduced labour requirements for weeding under CA. They further posit that weeds are only major problem where minimum tillage (MT) is adopted without crop residue mulching and diverse crop rotations. This thesis explores the effect of time under CA on weed population dynamics and crop growth under the recommended CA practices and actual smallholder farmer practice in semi-arid Zimbabwe. Assessment of weed and crop growth on a long-term CA experiment at Matopos Research Station revealed that the MT systems of planting basins and ripper tine were associated with higher early season weed density and biomass than conventional early summer mouldboard tillage (CONV) in both the fifth (cowpea phase) and sixth (sorghum phase) years of CA. This increased weed infestation within the first four weeks after planting in CA necessitated early weeding to provide a clean seedbed and avert significant crop yield loss. Maize mulching only suppressed early season weed growth in sorghum mostly at a mulch rate of 8 t ha-1 which is not a mulching rate that is attainable on most smallholder farms. However, the lower maize residue mulch rate of 4 t ha-1 was consistently associated with increased weed emergence and growth as from the middle of the cropping season in both crop species. The increased weed infestations under the mulch were probably due to the creation of ‘safe sites’ with moist conditions and moderate temperatures. The high weed growth under the mulch contributed to the low sorghum grain yield obtained under mulched plots. In addition, maize mulching was also associated with a less diverse weed community that was dominated by the competitive Setaria spp. and difficult to hoe weed Eleusine indica (L.) Gaertn. However, the weed community under CA was similar to that under CONV tillage with no evidence of a shift to the more difficult to control weed species. The increased early season weed growth and high weed pressure under CA meant that it was still necessary to hoe weed four times within the cropping season to reduce weed infestations and improve crop growth even after four years of recommended CA practices. Early and frequent weeding was effective in reducing weed growth of most species including Setaria spp. and E. indica demonstrating that on smallholder farms where labour is available hoe weeding can provide adequate weed control. The wider spacing recommended for use in CA contributed to the low cowpea and sorghum grain yields obtained under CA compared to CONV tillage. On smallholder farms in Masvingo District, the MT system of planting basin (PB) was the only conservation farming (CF) component adopted by farmers. There was no difference in the total seedling density of the soil weed seed bank and density of emerged weeds in the field in PB and conventional mouldboard ploughing done at first effective rains (CONV tillage). However, the first weeding in PB was done at least 15 days earlier (P < 0.05) than in CONV tillage suggesting high early season weed growth in PB relative to CONV tillage. As weed density did not decline with time in PB, weed management did not differ with increase in years under PB. Shortage of inputs such as seed and fertiliser was identified by smallholder farmers as the most limiting factor in PB crop production with the area under PB was equivalent to the seed and fertiliser provided by CARE International for most farmers. On this small area, weeds could be managed by available family labour. Double the maize grain yield was obtained in PB (mean: 2856 kg ha-1) due to improved weed management and soil fertility. However, the use of poorly stored composts was found to introduce weeds into some PB fields. The findings of this study demonstrated that weed pressure was still high and weed management were still a challenge under the practice recommended to smallholder farmers in Zimbabwe even in the sixth year of practice. There is, therefore, a need for research on the economic feasibility of using herbicides, intercropping and optimal crop density to ameliorate the high weed pressure under CA.
Thesis (PhD)--University of Pretoria, 2013.
Plant Production and Soil Science
unrestricted

A cell is considered to be the smallest unit of life. It carries out a variety of biochemical reactions through the activities of proteins and protein enzymes. In order to perform functions, proteins must be in their native folded state together with the correct environmental conditions. A slight change in pH or temperature could cause disruption to the electrostatic interactions within the protein, thus leading to conformational change and the loss of activity. Studies have shown that solubility could be enhanced by increasing the number of charges on the protein surface. And from the studies of extremophiles, we learned that the presence of non-polar aromatic residues could be a key for thermostable proteins. Thus, charges are important to determine the function and adaptation of proteins.Over the decades, large amount of protein sequence and structure information relating to molecular biology has been produced. By employing algorithms, computational and statistical techniques, it is possible to analyse these data to solve biological problems. Often these investigations are based mainly on sequences since their numbers outstrip the number of available structures. However, adding structures would allow us to investigate problems such as the relationship between charges, sequence, structure and functions, which is the aim of this study.In this thesis, the relationships between proteins and function were examined by various electrostatic features derived from charges and also geometric properties from structures. One interesting finding is that the averaged value of pH of maximum stability of proteins within a subcellular location was highly correlated to the pH of that subcellular compartment, which was due to pKas (of histidines), and their locations on the proteins. We also found that the size of the largest non-charged patch on the protein surface correlates with solubility and provides a predictor with a maximum accuracy of 76%. The use of novel charge-based methods shows little improvement in distinguishing between enzymes and non-enzymes. However, the method of using real charges with grid size of 1 angstrom has paved a way into the idea of using charges and dipoles pattern from enzyme active site to distinguish different enzymes. Finally, a web-tool for displaying conserved residues on 3D protein structure is made available to the public for identifying residues that may be of functional importance.

Conservation Agriculture (CA) has potential benefits to the soil, crop yield, and the environment including reducing runoff, enhancing water retention and preventing soil erosion, in addition to increasing soil carbon sequestration and reducing greenhouse gas (GHG) emissions. Although CA is widely adopted in some areas of the world, it is still not widely adopted by UK farmers. The first overall aim of this project was to investigate the effects of tillage practice and residue retention, on soil physical properties, crop yield and GHG emissions. For this purpose, a split-plot field experiment was established on the University of Nottingham farm between September 2014 and August 2016. The main plot treatment was residue retention while cultivation practices were applied to the sub-plots and included three different tillage systems: no-tillage, minimum-tillage and deep ploughing. We used a novel analytical tool, X-ray Computed Tomography, to characterise the 3-D soil pore network in conjunction with a number of other soil physical properties such as bulk density, penetration resistance and shear strength. A range of portable chambers were used to detect the GHG emissions from soil and from soil-plant systems as influenced by the tillage and residue treatments. Winter wheat yield was not affected by the tillage treatments or residue retention in the first year, but, in the second year, no-tillage caused a 10% reduction in triticale yield compared to minimum-tillage and traditional ploughing. Multiple regression analysis showed that the lower triticale yield was partially explained by higher soil strength in the no-tillage plots, together with lower soil moisture content in summer. Our results show that while there is potential for climate change mitigation from no-tillage when the Net Ecosystem Exchange is considered, this effect could not be observed from soil emissions only. The second aim of this project was to assess the current level of reduced tillage (RT) uptake by UK farmers and the constraints for further adoption. A postal questionnaire was conducted in January 2016. This questionnaire found that only 7.0% of the arable land in England is under no-tillage and 47.6% is under minimum-tillage. The adoption of RT increased with an increase in farm size as it was the most adopted on farms >400 ha. Moreover, RT was adopted most on combinable crop farms. Weed management and slugs were identified as main challenges for RT adopters. Increasing uptake of CA from current levels will probably require policy intervention including financial incentives for growers during the early stages of the transition from ploughing to CA. This will encourage farmers to buy RT equipment and may help them to cover any potential yield reduction, if occurred, before the CA system stabilisation.

Crop management practices, such as soil tillage and crop residue management, are land management activities with potentially large impacts on carbon (C) cycling and climate at the global scale. Improvements in crop management practices, such as conservation tillage or 'no-till' (NT), have been proposed as climate change mitigation measures because such practices may alter C cycles through increased sequestration of soil C in agricultural soils. Despite their potential importance, regional to global scale data are lacking for many crop management practices, and few studies have evaluated the potential impact of the full range of crop management practices on C cycling and climate at the global scale. However, monitoring of crop management practices is crucial for assessing spatial variations in management intensity and informing policy decisions. Inclusion of crop management practices in Earth system models used for assessing global climate is a key requirement for evaluating the overall effects of different crop management practices on C cycling and their potential to mitigate climate change. Studies in this dissertation seek to address these issues by: (1) evaluating the efficacy of remote sensing methods for monitoring differences in soil tillage and crop residue management practices in Iowa; (2) incorporating soil tillage practices into an Earth system model and assessing the potential for soil C sequestration and climate change mitigation through adoption of NT practices; (3) assessing the historical impact of including the full range of crop management practices (residue harvest, grain harvest, soil tillage, irrigation, and fertilization) on changes in C cycling associated with land use and land cover change (LULCC) to crops in an Earth system model. The remote sensing study found that performance of the minimum Normalized Difference Tillage Index (minNDTI) method for assessing differences in tillage and residue management was below average compared to previous studies, even when using imagery from both Landsat 8 and Sentinel-2A sensors. Accurate assessment of these practices using minNDTI was hindered by issues with image quality and inability to obtain sufficient cloud-free, time series imagery during the critical planting window. Remote sensing research aimed at obtaining regional to global scale data on tillage and residue management practices is likely to continue to face these issues in the future, but further research should incorporate additional sensors and assess the efficacy of the minNDTI method for multiple locations and years. Adoption of NT practices in the Community Land Model, which is the land component of the Community Earth System Model, resulted in a cumulative soil C sequestration of 6.6 – 14.4 Pg C from 2015 – 2100 under a future climate change scenario (Representative Concentration Pathway 8.5), and cumulative soil C sequestration was equal to approximately one year of present-day fossil fuel emissions. Adjusting for areas where NT is already practiced had minor impacts on cumulative soil C storage, reducing gains in soil C from NT adoption by 0.4 – 0.9 Pg C globally. These results indicate that soil C sequestration and potential for climate change mitigation through NT may be more limited than has been anticipated elsewhere. Soil C sequestration via NT adoption was highest in temperate regions of developed countries with high initial soil C contents, indicating these areas should be targeted for NT adoption. Simulating the full range of crop management practices in the Community Land Model resulted in an increase in C emissions due to LULCC of 29 – 38 Pg C compared to scenarios with generic crops and model defaults. Individual crop management practices with the largest impact on LULCC emissions were crop residue harvest (18 Pg C), followed by grain harvest (9 Pg C) and soil tillage (5 Pg C). Although implementation of crop residue harvest and soil tillage was extreme in this study, these results imply that Earth system models may underestimate emissions from LULCC by excluding the full range of crop management practices. Studies in this dissertation corroborate the importance of crop management practices for C cycling and climate, but further research on these management practices is needed in terms of data collection, improving process-level understanding, and inclusion of these practices in Earth system models.
Doctor of Philosophy

A two year study was initiated in 1999 at the Macdonald Campus Farm, on a 2.4 ha site consisting mainly of St-Amable sand to shallow loamy sand (Typic Endoaquent; Humic Gleysol). The site was planted to alfalfa ( Medicago sativa) prior to the establishment of the experimental design and has been planted to corn (Zea mays L.) since 1991. The experiment was set up as a randomized complete block design and consisted of three tillage levels (NT, no-till; RT, reduced tillage; and CT, conventional tillage) and two residue levels (-R, no residues; +R, with residues). This study was performed in order to ascertain the effect of these management systems on soil organic carbon (SOC), particulate organic matter carbon (POM-C), microbial biomass carbon (MBC) levels and soil physical properties. Soil physical properties measured included bulk density, saturated hydraulic conductivity (Ksat), dry and wet aggregate stability, total porosity, macroporosity at -1 kPa and -6 kPa of matric potential, and moisture content. Crop yield was also measured. Results indicated that lower rates of mineralization of POM-C under NT+R in the surface 0--10 cm led to significantly higher SOC at the same depth. There were no significant differences between treatments at the 10--20 cm depth. The MBC was not a good indicator of the differences in soil organic matter levels between treatments. No-till treatments had higher bulk densities, reduced total porosity and macroporosity, increased moisture content, and increased constant-head measured Ksat. Differences in Ksat as measured with the Guelph permeameter, were not significant between treatments, most likely due to increased earthworm activity in NT. There were no significant differences in crop yield in 1999, but a significantly wetter year in 2000 caused lower grain yields in NT+R compared to NT-R and CT+R.

Dark tobacco (Nicotiana tabacum L.) has historically been produced usingconventional tillage practices. Soil is cultivated multiple times throughout a growing season leading to an increased incidence of soil erosion. No-till systems have been growing in popularity with the advent of new technology that has enabled the practice to be performed effectively and efficiently. With the recent expansion of no-till practices throughout the agricultural community, many crops have had success in producing comparable yields while reducing input costs and saving soil resources. For this experiment, a traditional tobacco transplanter was modified for use in a no-till environment. All modifications were fabricated without using specialty tools and made possible to be removed if desired or necessary. Frame extensions were designed and built to accommodate row cleaners and coulters. Tillage shanks were also added to aid in optimal furrow formation. Double-disc opening shoes replaced the original round point shoes and the curved edges of the rear drive wheels were removed, creating a flat surface to increase soil contact. Experimental no-till plots in fescue sod and soybean chaff residues were conducted alongside conventional tillage plots at the Western Kentucky University Agricultural Research and Education Complex in summer 2011. Five treatments, one conventionally tilled (Conv) and four no-till, were replicated three times within a randomized complete block design and used to determine the efficacy of transplanter modifications (consistency of depth, furrow closure, observed plant damage), survival of the transplants, and the amount of residue displacement. The four no-till treatments utilized different combinations including: coulter, row cleaner and shank (CRS), row cleaner and shank (RS), coulter and shank (CS), and shank only (S). These treatments demonstrated the functionality of each combination in comparison to conventional treatments. No treatment performed equally well in both residue locations. Plots in fescue residue utilizing a combination of coulter, row cleaner, shank (CRS), exhibited the lowest amount of root exposure, highest survival rate, and comparable cured weight when compared to conventionally tilled treatments. In soybean residue plots, the treatment operating with row cleaners and shanks (RS) had equivalent amounts of furrow closure to conventionally tilled plots. Pairing specific modification combinations with previous crop residue can provide furrow closure, transplant survival, and cured yield equivalent to conventionally tilled dark tobacco.

Here, we present a study of polar residues within the membrane core of alpha-helical membrane proteins. As expected, polar residues are less frequent in the membrane than expected. Further, most of these residues are buried within the interior of the protein and are only rarely exposed to lipids. However, the polar groups often border internal water filled cavities, even if the rest of the sidechain is buried. A survey of their functional roles in known structures showed that the polar residues are often directly involved in binding of small compounds, especially in channels and transporters, but other functions including proton transfer, catalysis, and selectivity have also been attributed to these proteins. Among the polar residues histidines often interact with prosthetic groups in photosynthetic-and oxidoreductase-related proteins, whereas pro-lines often are required for conformational changes of the proteins. Indeed, the polar residues in the membrane core are more conserved than other residues in the core, as well as more conserved than polar residues outside the membrane. The reason is twofold; they are often (i) buried in the interior of the protein and (ii) directly involved in the function of the proteins. Finally, a method to identify which polar residues are present within the membrane core directly from protein sequences was developed. Applying the method to the set of all human membrane proteins the prediction indicates that polar residues were most frequent among active transporter proteins and GPCRs, whereas infrequent in families with few transmembrane regions, such as non-GPCR receptors. Proteins 2011; 79: 79-91.

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This research is concerned with the detection and removal of hazardous biocide residues from historic applications to herbarium collections. There are two main aims: • To develop a rapid, cost-effective and non-destructive screening method for identifying toxic residues on herbarium sheets; and • To establish the most suitable decontamination method for the removal of naphthalene from herbarium collections, maintaining the integrity of the specimen. The research outlines how the presence of fluorescent marks on specimen sheets throughout the herbarium, at Amgueddfa Cymru- National Museum Wales (AC-NMW), is indicative of mercury(II) chloride contamination. Compelling evidence is given to support the hypothesis that the observed fluorescence is due to the reduction of Hg(II) to Hg(I) during the oxidative degradation of cellulose, occurring as part of the natural ageing process. The rate of fluorescence development is shown to be increased by the presence of naphthalene, and is estimated to take at least 30 years to develop. From the results obtained, it is evident that a hand-held UV-A lamp can provide a rapid and effective method of identifying samples within a collection that are contaminated with mercury, thus providing a rapid and economical means to prioritise which collections require immediate re-mounting. Furthermore, this method will enforce the implementation of safe, standard procedures to protect personnel and visitors when handling the collections, plus enable the removal of a large amount of hazardous chemical from the herbarium environment. It is also demonstrated, through decontamination tests, that the air-drying of contaminated specimen sheets is a more efficient method of removing naphthalene, than either freeze-drying or oven-drying. It is also the most cost-effective, and the least damaging to the specimen. It is shown that the efficacy of the decontamination is dependent upon the paper type. Thin, unfinished, papers are more efficient at losing naphthalene than the heavier, finished and coated papers, as their porous structure allows the naphthalene to remain more mobile. These results provide important information about which specimen sheets are more likely to be successfully decontaminated by the air-drying procedure and can inform the selection and prioritisation process.

This thesis presents the construction, the analysis and the verication of compact residual discretizations for the solution of conservation laws on unstructured meshes.

The schemes considered belong to the class of residual distribution (RD) or fluctuation splitting (FS) schemes.

The methodology presented relies on three main elements: design of compact linear first-order stable schemes for linear hyperbolic PDEs, a positivity preserving procedure mapping stable first-order linear schemes onto nonlinear second-order schemes with non-oscillatory shock capturing capabilities, and a conservative formulation enabling to extend the schemes to nonlinear CLs. These three design steps, and the underlying theoretical tools, are discussed in depth. The nonlinear RD schemes resulting from this construction are tested on a large set of problems involving the solution of scalar models, and systems of CLs. This extensive verification fills the gaps left open, where no theoretical analysis is possible.

Numerical results are presented on the Euler equations of a perfect gas, on a two-phase flow model with highly nonlinear thermodynamics, and on the shallow-water equations.

On irregular grids, the schemes proposed yield quite accurate and stable solutions even on very difficult computations. Direct comparisone show that these results are more accurate than the ones given by FV and WENO schemes. Moreover, our schemes have a compact nearest-neighbor stencil. This encourages to further develop our approach, toward the design of very high-order schemes, which would represent a very appealing alternative, both in terms of accuracy and efficiency, to now classical FV and ENO/WENO discretizations. These schemes might also be very competitive with respect to very high-order DG schemes.
Doctorat en sciences appliquées
info:eu-repo/semantics/nonPublished

In this work we review 12 years of developments in the field of residual based discretizations for hyperbolic problems and their application to the solution of the shallow water equations. Fundamental concepts related to the topic are recalled and he construction of second and higher order schemes for steady problems is presented. The generalization to time dependent problems by means of multi-step implicit time integration, space-time, and genuinely explicit techniques is thoroughly discussed. Finally, the issues of C-property, super consistency, and wetting/drying are analyzed in this framework showing the power of the residual based approach.

This thesis contributes to the literature in the finance and accounting field throughout its three empirical chapters. The first empirical chapter contributes to the literature on accounting conservatism in several ways; first, it investigates the accounting conservatism of US insurance companies using four measures, namely, non-operating accruals, skewness of earnings and cash flows, book to market ratio and asymmetric timeliness measures. Second, this paper compares these four measures in order to determine the association and differences between them. Finally, the level of accounting conservatism of the insurance companies is compared to that of a sample of commercial banks to check whether they have similar levels of accounting conservatism. The results of the first chapter suggest that the changes in accounting performance, as measured by return over assets, can be partly explained by accounting conservatism, since it is measured by the accumulation of non-operating accruals, skewness of operating cash flow and accruals, book to market ratio, adjusted book to market ratio and Basu's asymmetric measure. All of these four measures give robust evidence that insurance companies' accounts tended to be conservative for the whole sample period, and that the level of conservatism has risen over the years. More interestingly, a t test for the differences in means suggests that accruals conservatism show on average a higher level of accounting conservatism than book value conservatism does. Finally, our results, based on a constant sample consist of 92 banks and 46 insurance companies whose data are available for all the sample years; they suggest that both insurance companies and banks have similar levels of accounting conservatism due to their similar reporting characteristics. The second empirical chapter contributes to the existing literature on equity valuation in two ways. First, it confirms the importance of imposing linear information dynamics when predicting the equity values of insurance companies, because the restricted models result in fewer error metrics. Second, it highlights the role of the accruals components in the equity valuation of US insurance companies by demonstrating that the incorporation of accrual components in the residuals income valuation model suggested by Ohlson (1995) has smaller error metrics than those of aggregate net income. Our results are based on a sample of US insurance companies, which consists of 718 firm-year observations over the period from 2001 to 2012. For instance, our results suggest that total accruals, changes in insurance reserve, changes in account receivables, and deferred acquisition costs have an incremental ability to predict equity market value over abnormal earnings and book values. Furthermore, the predictive ability of changes in insurance reserves is higher than the predictive ability of changes in account receivables and the change in deferred acquisition costs without imposing the LIM structures. However, when the LIM structure is imposed the predictive ability of changes in deferred acquisition costs is higher than the predictive ability of both changes in accounts receivable and changes in insurance reserves. Our final empirical chapter contributes to the literature on accounting anomalies by investigating the value to price anomaly (V/P), where the fundamental value (V) is estimated using the residual income valuation model. Motivated by the findings of Hwang and Lee (2013), Fama and French (2015), and Fama and French (2016), Chapter Four asks whether V/P strategies reflect the risks factor or whether this is better explained by market inefficiency, and whether Fama and French's five-factor model can explain the excess return of V/P. To answer the previous questions we use data from the merger of COMPUSTAT, CRSP, I/B/E/S for all the non-financial firms listed in AMEX, NYSE, and NASDAQ during the period from 1987 to 2015. Our findings suggest that the V/P ratio is positively correlated to future stock returns after controlling for several firm characteristics, which are known to be proxies of common risks. Our results indicate that the omission of risk factors is not likely to be an explanation of the V/P effect. To answer the second question, we compare the performances of different asset pricing models by calculating the GRS F-statistics. Our findings clearly indicate that the five-factor model of Fama and French performs better than either the CAPM or the traditional Fama and French three factor model. These results confirm that the excess returns of V/P strategy vary due to the differences in size, the B/M ratio, operating profit and betas across quintile portfolios. However, these factors cannot explain all the variation in excess returns; moreover, the stocks in the high V/P may be riskier than the stocks in the low V/P portfolios in certain other dimensions.

La surdité de perception est généralement la conséquence de la mort des cellules ciliées et de la dégénérescence supplémentaire des innervations afférentes induite par une absence de stimulation. Les indications de l’implant cochléaire se sont élargies en direction des patients sourds qui présentent un reliquat d’audition exploitable dans les fréquences graves. La persistance d’un reliquat auditif suffisant après l’intervention permet parfois une stimulation électrique acoustique, amplifiée acoustique sur les fréquences graves préservées, et électrique sur les fréquences aiguës. Actuellement, plusieurs protocoles de préservation de l’audition sont en investigation. Chaque protocole vise à appliquer des procédures qui minimisent les deux mécanismes du traumatisme, à savoir trauma immédiat et trauma différé. En particulier, une insertion atraumatique du porte-électrode (Flex EAS et Flex Soft ; Med-El) a été proposée pour minimiser le traumatisme chirurgical intracochléaire. L’application local et concomitante de médicament devrait améliorer la tolérance du tissu et donc réduire les dommages intracochléaire au niveau cellulaire. Un cathéter (Med-El) intra cochléaire pour la délivrance de médicaments intracochléaire a été développé, destiné à l’utilisation d’agents pharmacologiques in situ avant l'insertion du porte-électrode. Les propriétés mécaniques de ce cathéter n’induit pas de traumatisme dans la cochlée. Une insertion séquentielle de cathéter et de porte-électrodes est réalisable et souvent atraumatique
Sensorineural deafness is generaly the result of hair cell death and additional degeneration of afferent innervation. In recent years the candidacy criteria for cochlear implantation have been expanding, and now include patients with severe to profound high-frequency hearing loss along with mild to moderate low-frequency loss. The single most important prerequisite for providing both electric and acoustic stimulation in the same ear is the preservation of acoustic hearing following the surgical procedure. Currently, several hearing preservation protocols are under investigation. Each protocol attempts to implement procedures that minimize both immediate and delayed mechanisms. Specifically, atraumatic approaches and electrode insertions (Flex EAS and Flex Soft) have been proposed that aim at minimizing the surgical aspect of intracochlear trauma. The concomitant application local of drugs should enhance tissue tolerability and thus reduce intracochlear damage on a cellular level. Acute and topical, intracochlear drug delivery prior to electrode array insertion with a disposable single-use catheter (Med-El) has been evaluated and developed. The flexible properties of this catheter are enough to be inserted without trauma in the cochlea. Sequential insertion of intracochlear catheters and electrode arrays is feasible and often atraumatic

L’Agriculture de conservation (AC) repose sur trois principes: le minimum de travail du sol, la couverture permanente du sol et la diversification des espèces cultivées. Elle a été introduite vers la fin des années 90 dans la région du lac Alaotra, Madagascar, dans l’objectif d’augmenter la productivisté de l’agriculture pluviale qui, généralement, pâtit des problèmes liés à la faible fertilité des sols, aux contraintes hydriques et à l’enherbement. L’objectif principal de la thèse consiste à quantifier et caractériser les impacts des fonctions agro-écologiques de l’AC dans l’amélioration du rendement en riz pluvial par rapport aux pratiques conventionnelles (CT). Une revue de la littérature sur les fonctions agro-écologiques du mulch en fonction de leur quantité retenue sur la parcelle a tout d’abord montré que la quantité de couverture nécessaire va dépendre essentiellement des fonctions agro-écologiques attendues. Une quantité de couverture de 2 à 3 t ha-1 permet d’obtenir des effets très nets en ce qui concerne l’amélioration de l’infiltration de l’eau, la limitation du ruissellement et de l’érosion du sol. En revanche, les données sur le contrôle de l’enherbement, la disponibilité des nutriments ainsi que la faune du sol en fonction de la quantité de mulch étaient très variables, suggérant l’interaction de ses fonctions agro-écologiques avec d’autres facteurs, notamment le type de résidus et les conditions pédoclimatiques. Une première expérimentation dont l’objectif était la quantification des effets physiques du mulch sur l’enherbement, avec différentes quantités de résidus de 0 à 45 t ha-1 a montré que l’émergence et la biomasse des adventices sur les parcelles couvertes dépend essentiellement de la quantité et de la distribution de la pluviométrie durant la saison culturale. L’émergence ainsi que la biomasse des mauvaises herbes diminuent en général avec l’augmentation de la quantité de mulch maintenue sur les parcelles. Toutefois, une quantité de résidus de l’ordre de 10 t ha-1 est nécessaire pour réduire significativement la pression des adventices sur le riz par rapport à un sol nu dans les conditions de notre dispositif expérimental. Un deuxième dispositif maintenu durant 6 ans (2009/10 à 2014/15), combinait une rotation biennale de maïs + dolique // riz et une rotation triennale de maïs + stylosanthes // stylosanthes // riz ; trois modes de gestion du sol et des résidus et deux niveaux de fertilisation. Deux niveaux d’enherbement en split plot ont été ajoutés en 2013/14 et 2014/15. L’amélioration du rendement en riz sur les parcelles en AC par rapport aux parcelles en CT est essentiellement liée à une diminution de la pression des adventices sur les parcelles AC pendant la période de végétation du riz. La dynamique de l’eau dans le sol ainsi que la dynamique de l’azote minéral sont fortement influencées par le régime pluviométrique et ne différent généralement pas entre AC et CT. Enfin, l’analyse de stabilité et l’écart de rendement au potentiel utilisés pour étudier les variations de rendements en riz sur les 6 saisons culturales du second dispositif expérimental ont montré que les effets des traitements étaient en interaction avec d’autres facteurs probablement liés à la variabilité spatiale du sol sur le dispositif expérimental. Les résultats de cette étude nous suggèrent de tenir compte aussi bien des fonctions agro-écologiques du mulch attendues que les régimes pluviométriques lors de la promotion d’un système AC pour améliorer la productivité des cultures. L'AC avec une quantité de résidus généralement retenus dans les parcelles de l'agriculteur (i.e. 1 - 2 t ha-1) serait efficace pour lutter contre le ruissellement et l'érosion. Cependant, des quantités supplémentaires de résidus, qui pourraient être produites avec l’introduction de rotations culturales avec une forte production de biomasse, seraient nécessaires pour lutter efficacement contre les adventices et diminuer les charges liées au sarclage
Conservation agriculture (CA) is based on the principles of minimum soil disturbance, permanent soil cover and diversification of crop species grown in rotations and/or associations. CA was introduced in the late 90s in the Lake Alaotra region, Madagascar, in order to improve rainfed crop productivity which is commonly constrained by low soil fertility, soil water stress and weed infestation. The main objective of this study was to quantify and understand the impact of CA on rainfed rice productivity as compared to the practice of conventional tillage (CT). First, a review of literature was conducted on the agro-ecological functions of mulching with crop residues in relation to their quantity. The literature review showed that the optimal amount of residues required principally depends on the agro-ecological function searched for. Residue amounts of 2 to 3 t ha-1 had clear positive effects in terms of improving water infiltration and limiting water runoff and soil erosion. On the other hand, results on weed control, nutrient availability and soil fauna in relation to the amount of mulch were highly variable, suggesting the interaction of these agro-ecological functions with other factors, including residue type and soil-climate conditions. Second, two field experiments were monitored at the research center of FOFIFA in the Lake Alaotra region. A first experiment aiming at quantifying the physical effect of a mulch of crop residues on weed infestation, with amounts of surface residues ranging from 0 to 45 t ha-1 showed that the emergence and biomass of weeds on mulched plots depend mainly on the quantity and distribution of rainfall during the cropping season. Overall, weed emergence and biomass decreased with increasing amounts of mulch. However, a large quantity of residues, i.e. in the order of 10 t ha-1, was required to significantly (p<0.05) reduce weed pressure as compared to a bare soil under the agro-ecological conditions of our experiments. The second experiment was conducted during six years (2009/10 to 2014/15), and a 2-year rotation of maize + Dolichos lablab // rice and a 3-year rotation of maize + Stylosanthes guianensis // S. guianensis // rice were combined with three soil/residue management practices and two level of fertilization. Two levels of weed pressure were added as split-plot in 2013/14 and 2014/15. Higher rice grain yields on CA plots as compared to CT plots in the fifth and sixth year of the CA practice were mainly related to a decline of weed pressure under CA. Soil water and mineral nitrogen dynamics did not differ markedly between CA and CT and were strongly influenced by the rainfall pattern. Finally, the use of the concept of stability analysis and the yield gap approach to analyze the variation of rice yield under the 6 crop seasons from 2009/10 to 2014/15 showed that the effects of treatments including crop rotation, soil and residue management, and fertilization levels interact with other factors likely related to the spatial variability of the experimental design. Results of our study suggest that both agro-ecological function of mulch searched for and rainfall conditions should be taken into account when promoting CA systems to improve crop productivity in the Lake Alaotra region. Practicing CA with typical amounts of residues that are produced on farmer’s field (i.e. 1 – 2 t ha-1) is sufficient to control water runoff and soil erosion. However, extra amounts of crop residues are required to effectively control weed infestation. These extra amounts could be produced with the introduction of high biomass-producing crop rotations and could decrease the labor pressure from weeding

Utilise a faible dose en raison de sa toxicite propre, l'ion nitrite (no#2#) est, avec son precurseur l'ion nitrate (no#3#), l'un des additifs les plus courants des produits de charcuterie et salaisons. Il le doit, tout d'abord, a ses proprietes inhibitrices sur la croissance du bacille botulique, mais aussi a son action sur la couleur. (nitrosomyoglobine) et sur la flaveur des produits carnes, par l'intermediaire de nombreux derives s, n ou c-nitroses qu'il engendre. Outre les interferences d'ordre chimique auxquelles peut etre confrontee la reaction de diazotation (griess), qui est a la base de la methode officielle, cette derniere ne dose que le nitrate et le nitrite. L'interet de la methode mise au point est precisement de permettre le dosage selectif differentiel du nitrite et des derives nitroses par denitrosation et mesure de l'oxyde d'azote (no) par chimiluminescence. La technique a ete tout d'abord validee sur des solutions pures de nitrite et de derives nitroses, puis sur des echantillons de charcuterie a faible teneur en gras. Dans un deuxieme temps, elle a ete appliquee a l'analyse d'echantillons de longes de porc ayant subi differents traitements technologiques (salage, fumage, sechage, stockage. . . ) dans le but d'evaluer l'incidence de ces differentes modalites sur l'evolution du nitrite et de ses derives dans les viandes. La derniere partie de ce travail a ete consacree a la mise au point du couplage clhp-denitrosation-chimiluminescence, susceptible de permettre une separation prealable des derives nitroses solubles et leur dosage differentiel ulterieur

Ce travail de thèse, propose un schéma numérique d'ordre élevé, distribuantle résidu (RD) pour l'approximation d'un problème hydro-sédimentairehyperbolique non conservatif, couplant les modèles de Grass et de Saint-Venant. Il fait appel à des méthodes de Runge-Kutta à variation totale diminuanteet de stabilisation (méthode de décentrement amont, dit Upwind),avec ou sans adjonction de limiteurs et présente de bonnes propriétés.L'une des facettes importantes de ce qui a été réalisée, repose sur la conceptionet le développement d'un programme Python 2D-espace, sous la formed'un logiciel faisant appel à un ensemble de modules créés pour l'occasion.Le développement du code de calcul, qui se propose d'approcher la solutiondu problème hydro-sédimentaire, a été e_ectué avec une orientation Objetet pour être e_cace sur calculateur parallèle (utilisant le parallélisme multithreadsOpenMP). L'une des particularités du schéma numérique dans cecadre, est liée à son application à des quadrangles.Un programme 1D-espace, qui se présente également sous forme de logiciel,a aussi été mis en place. Pour des raisons de portabilité et d'e_catité, il aété écrit multilangages (Python-Fortran : via numpy.ctypes pour Python etvia l'interface standard de Fortran pour C). Le schéma RD avec ou sansadjonction de limiteurs de _ux, a été implémenté à la manière d'un schémaprédicteur-correcteur. Des comparaisons avec d'autres schémas ont été e_ectuées a_n de montrer son e_cacité, son ordre de précision élevé a été mis enévidence, et la C-propriété a été testée. Les tests ont révélé que, pour le casd'un transport d'un pro_l sédimentaire parabolique, c'est le limiteur de _uxMUSCL MinMod, qui est le plus adapté parmi ceux testés.Dans le cas scalaire, des tests numériques ont été réalisés a_n de validerle second ordre de précision
The present work, proposes a high order Residual Distribution (RD) numericalscheme to solve the non conservative hyperbolic problem, coupling Shallow Water and Grass equations. It uses Total Value Diminishing Runge Kutta and stabilisation Upwind methods, with or without limiters. It also has some good properties.A part of the work realised in this thesis, is about the conception and the developpement of a 2D-space Python program, under the form of a software,using a set of moduls created for the occasion. the code developpement, whichis said to approach the _uid-sediment model, coupling Shallow-Water and sedimentequations, has been made with an Object orientation and in orderto be e_cient on parallel architecture (using multithreads OpenMP parallelism). One of the features of the scheme in this case, is due to its application on quadrangles.A 1D-space program, also writen as a software, has been estabished. In order to be portable and e_cient, It has been developped multilinguals (Python- Fortran : by numpy.ctypes for Python and by standart interface FORTRAN for C). The RD scheme with or without Flux Limiters, has been implemented like predictor-corrector one. Comparisons with other schemes results have been realised, in order to show its e_ciency, moreover its high order accuracy has been focus on, and the C-proprerty has been tested. The tests show that MUSCL MinMod _ux limiters, is the most adaptated for a dune test case, between all tested.In the scalar case, numerical tests have been realised, for validating the secondorder of accuracy

La simulation numérique est aujourd'hui un outils majeur dans la conception des objets aérodynamiques, que ce soit dans l'aéronautique, l'automobile, l'industrie navale, etc... Un des défis majeurs pour repousser les limites des codes de simulation est d'améliorer leur précision, tout en utilisant une quantité fixe de ressources (puissance et/ou temps de calcul). Cet objectif peut être atteint par deux approches différentes, soit en construisant une discrétisation fournissant sur un maillage donné une solution d'ordre très élevé, soit en construisant un schéma compact et massivement parallélisable, de manière à minimiser le temps de calcul en distribuant le problème sur un grand nombre de processeurs. Dans cette thèse, nous tentons de rassembler ces deux approches par le développement et l'implémentation de Schéma Distribuant le Résidu (RDS) d'ordre très élevé et de compacité maximale. Ce manuscrit commence par un rappel des principaux résultats mathématiques concernant les Lois de Conservation hyperboliques (CLs). Le but de cette première partie est de mettre en évidence les propriétés des solutions analytiques que nous cherchons à approcher, de manière à injecter ces propriétés dans celles de la solution discrète recherchée. Nous décrivons ensuite les trois étapes principales de la construction d'un schéma RD d'ordre très élevé : \begin{itemize} \item la représentation polynomiale d'ordre très élevé de la solution sur des polygones et des polyèdres; \item la description de méthodes distribuant le résidu de faible ordre, compactes et conservatives, consistantes avec une représentation polynomiale des données de très haut degré. Parmi elles, une attention particulière est donnée à la plus simple, issue d'une généralisation du schéma de Lax-Friedrichs (LxF); \item la mise en place d'une procédure préservant la positivité qui transforme tout schéma stable et linéaire, en un schéma non linéaire d'ordre très élevé, capturant les chocs de manière non oscillante. \end{itemize} Dans le manuscrit, nous montrons que les schémas obtenus par cette procédure sont consistants avec la CL considérée, qu'ils sont stables en norme $\L^{\infty}$ et qu'ils ont la bonne erreur de troncature. Même si tous ces développements théoriques ne sont démontrés que dans le cas de CL scalaires, des remarques au sujet des problèmes vectoriels sont faites dès que cela est possible. Malheureusement, lorsqu'on considère le schéma LxF, le problème algébrique non linéaire associé à la recherche de la solution stationnaire est en général mal posé. En particulier, on observe l'apparition de modes parasites de haute fréquence dans les régions de faible gradient. Ceux-ci sont éliminés grâce à un terme supplémentaire de stabilisation dont les effets et l'évaluation numérique sont précisément détaillés. Enfin, nous nous intéressons à une discrétisation correcte des conditions limites pour le schéma d'ordre élevé proposé. Cette théorie est ensuite illustrée sur des cas test scalaires bidimensionnels simples. Afin de montrer la généralité de notre approche, des maillages composés uniquement de triangles et des maillages hybrides, composés de triangles et de quadrangles, sont utilisés. Les résultats obtenus par ces tests confirment ce qui est attendu par la théorie et mettent en avant certains avantages des maillages hybrides. Nous considérons ensuite des solutions bidimensionnelles des équations d'Euler de la dynamique des gaz. Les résultats sont assez bons, mais on perd les pentes de convergence attendues dès que des conditions limite de paroi sont utilisées. Ce problème nécessite encore d'être étudié. Nous présentons alors l'implémentation parallèle du schéma. Celle-ci est analysée et illustrée à travers des cas test tridimensionnel de grande taille. Du fait de la relative nouveauté et de la complexité des problèmes tridimensionels, seuls des remarques qualitatives sont faites pour ces cas test : le comportement global semble être bon, mais plus de travail est encore nécessaire pour définir les propriétés du schémas en trois dimensions. Enfin, nous présentons une extension possible du schéma aux équations de Navier-Stokes dans laquelle les termes visqueux sont traités par une formulation de type Galerkin. La consistance de cette formulation avec les équations de Navier-Stokes est démontrée et quelques remarques au sujet de la précision du schéma sont soulevées. La méthode est validé sur une couche limite de Blasius pour laquelle nous obtenons des résultats satisfaisants. Ce travail offre une meilleure compréhension des propriétés générales des schémas RD d'ordre très élevé et soulève de nouvelles questions pour des améliorations futures. Ces améliorations devrait faire des schémas RD une alternative attractive aux discrétisations classiques FV ou ENO/WENO, aussi bien qu'aux schémas Galerkin Discontinu d'ordre très élevé, de plus en plus populaires.

碩士
國立臺灣大學
工程科學及海洋工程學研究所
99
Protein-RNA interactions play a vital role in many stages of gene expression such as pre-mRNA synthesis, mRNA splicing and translation. It is generally believed that binding domains or binding motifs enable RNA-binding proteins to recognize their target RNA. Since the corresponding nucleic acid type and the structure level recognized can be quite diverse, predicting RNA-binding residues from primary structure of proteins is indeed a challenging task. In this thesis, we continue the work of ProteRNA and develop two classifiers, namely support vector machine (SVM) and random forests (RF), with the predicted protein disorder added as a new feature descriptor. For the post-processing procedure, we build a discriminator in order to improve the pattern quality by distinguishing RNA-binding residues from other functionally important ones in conserved regions. When considering the dataset preparation effects and variance in binding sites, the two classifiers achieve Matthew’s correlation coefficient (MCC) of 0.5288 and 0.4698 using five-fold cross-validation. Our approach outperforms other predictors which provide online service. Testing on the independent test dataset, the SVM model achieves an accuracy of 92.12%, sensitivity of 38.10%, specificity of 97.47%, precision of 59.89%, F-score of 0.4657 and MCC of 0.4381, while the RF model ranks second only to SVM, it achieves an accuracy of 90.08%, sensitivity of 34.47%, specificity of 95.59%, precision of 43.62%, F-score of 0.3851 and MCC of 0.3346. We observe the measure trend in machine learning methods for datasets based on different sequence identities, and discuss the origin of performance increment and bottleneck. We find out that the homologous sequence, or even remote homologous in the same dataset as query sequence will probably make prediction result closer to the distribution of real binding sites. Besides, a method that identifies the nearest neighbor by sequence alignment and determines its binding residues accordingly may perform better than machine learning methods trained on PSSM in some cases. Nevertheless, when dealing with novel protein sequences, the excellent performance of machine learning methods shows great generalization ability.

博士
國立交通大學
生物資訊及系統生物研究所
105
Functionally or structurally important residues such as catalytic sites in a protein are usually evolutionary conserved. To identify these conserved residues, a set of homolog sequences are generally used to calculate sequence conservation scores. Interestingly, the sequence conservation scores were found to be highly correlated with residue structural environments in a protein structure. Therefore, we could estimate evolutionary information from a single protein structure even without information from homolog proteins. In 2008, our lab proposed a residue structural environment of the WCN model, which can describe the packing extent of every residue in a protein structure. The WCN model was then used to explore the relationships between protein structure and sequence conservation in 2012. Recently, we proposed another structural model named relative space of Voronoi volume (RSV), which describes available space for every residue. RSV is only affected by nearest residues while WCN considers longer-range interactions. We will focus on RSV and WCN models in this thesis. Moreover, solvent exposure, depth, dynamic properties, or more sophisticated interactions of van der Waals or electrostatic force in protein structures will be introduced. With these structural descriptors, we can quantify the residue-level information with a number representing structural environments. Using the dataset of 554 enzymes, we explore the relationships between all structural environments and sequence conservation. Furthermore, we could use these relationships to identify functionally important residues or assess the quality of a protein model. With such detailed analysis of structural environments in this study, we believe there will be more applications for structural environments related to protein functionality, protein stability, structure prediction, or protein evolution in future research.

博士
國立交通大學
生物資訊及系統生物研究所
105
Proteins interact with other proteins to perform their biological functions. Thus, the knowledge of protein-protein interfaces is valuable in understanding molecular mechanisms. Recently, we have observed that structural packing profiles of proteins have moderate correlations with their corresponding conservation profiles. However, some proteins were found to have low correlations between these two profiles, where structural packing profiles of the proteins were computed using a weighted contact number (WCN) model with the structures of single proteins. To better understand the characteristics in protein-protein interfaces, we explored the relationship between structural packing and residue conservation in protein-protein interfaces from 344 non-homologous subunits of 328 enzymes complexes. These subunits compose three datasets: Set I, Set A, and Set B. In Set A, catalytic sites of complexes are in the interfaces and consist of residues from multiple subunits; in Set B, catalytic sites of complexes are not in the interfaces and consist of residues from single subunits. We found that interface residues in three datasets tend to have high WCN scores (i.e., low structural packing). However, interface residues of Set B tend to have high conservation scores (i.e., lowly conserved). The tendency is different from those of the other datasets. This could be that complexes of Set B have weaker functional and structural constraints on their evolutionary processes than those of the other datasets in the condition that the enzymatic functions of the complexes are maintained. Surprisingly, the results show that the interface residues have distinct distributions of differences between the WCN scores and the conservation scores from the non-interface residues. Also, the WCN scores of the interface residues tend to be higher than their corresponding conservation scores. Furthermore, using a difference between a WCN score and a conservation score of a residue to detect the protein-protein interfaces, noteworthy sensitivity was obtained. This study provides interface properties in structural packing and residue conservation and elucidates the relationship between the structural packing and the residue conservation in interfaces of individual subunits.

博士
國立交通大學
生物資訊及系統生物研究所
105
During evolution, substitutions at individual residues within amino acid sequences arise under the constraints of structure folding, protein function, and the protein–protein interactions. Amino acid sequences generally fold into unique, stable, and well-ordered conformations so that the resulting proteins can carry out their specific functions. As such, residues that are important for function and structural stabilization are generally highly conserved in terms of both sequence and structure. Recent studies have discussed the structural constraints imparted by site-specific substitutions, and amino acid sequence conservation was found to correlate with solvent accessibility and the local packing density such as weighted contact number. The relationship between sequence conservation, site-specific substitution rates derived from multiple sequence alignment, and the weighted contact number, local packing density derived from three-dimensional structure, revealed that the evolution constraint of protein sequence and structure properties were correlated. In this study, we assessed the relationship between the packing density profiles drawn out from similar protein domain structures in SCOP superfamily with the relationship of remote homologs, and the results showed that similar structures had similar weighted contact number profiles, and demonstrated that the packing density profiles could reflect the structural constraints. Then, we compared the site-specific substitution rate profiles of two proteins and their structures, and the results showed that similar conservation profiles could be linked to similar structures. The evolution constraints of protein sequence and structure were not only related to each other in a protein, but also were interrelated in different proteins. The protein sequence and structure restricted by evolution constraints lead to that the binding regions tend to be conserved in sequence and structure and the interacting residues involved are usually in close three-dimensional space. In this study, we analyzed the protein structure, local packing density and residue constitute of metal ion-binding sites, including Ca2+, Cu2+, Cu+, Fe3+, Fe2+, Mg2+, Mn2+, Zn2+, Cd2+, Ni2+, Hg2+, and Co2+. The analysis of local packing density of metal ion-binding sites revealed that the metal ion-binding sites tend to be more crowded in proteins. Our result showed that the distributions of local packing density of metal ion-binding residues were distinct from those of non-metal ion-binding residues. The results showed that there were distinct different binding patterns of these twelve kinds of metal ion-binding sites, indicating the conservation of structure and sequence in metal ion-binding residues. According to the conserved patterns of structure and residue, we further developed a method to predict the metal ion-binding residues and build the model of metal ions docking by using fragment transformation method, and built up the MIB server (Metal Ion Binding sites prediction and docking server, http://bioinfo.cmu.edu.tw/MIB/) for not only twelve metal ion–binding sites prediction but also metal ions docking.

碩士
國立交通大學
生物資訊及系統生物研究所
103
蛋白質序列中序列保留性高的氨基酸常常在功能上或結構上是重要的. 每個氨基酸在序列保留的程度上通常會受到它們的本身的物理性質所影響. 其中一個性質是緊湊的蛋白質結構中的自由空間. 在這次的研究中, 我們提出一個基於Voronoi體積的方法來量化氨基酸周圍的自由空間, 名叫Relative Space of Voronoi (RSV). 根據計算序列保留度和結構特性的相關係數, 結果顯示沿著序列上的氨基酸其序列保留度上的變化和RSV有很好的相關性. 我們的結果提出另一種方式來研究序列保留度和結構特性之間的關係.

Although products of coal combustion (PCCs) such as coal ash are currently exempted from classification as a hazardous waste in the United States under the 1976 Resource Conservation and Recovery Act (RCRA), the U.S. Environmental Protection Agency (EPA) is now revising a proposed rule to modify disposal practices for these materials in order to prevent contamination of ground- and surface water sources by leached trace elements. This paper analyzes several aspects of EPA’s scientific reasoning for instating the rule, with the intent of answering the following questions: 1) Are EPA’s cited values for PCC production and disposal accurate estimates of annual totals?; 2) In what ways can EPA’s leaching risk modeling assessment be improved?; 3) What is the total quantity of trace elements contained within all PCCs disposed annually?; and 4) What would be the potential costs and feasibility of reclassifying PCCs not under RCRA, but under existing NRC regulations as low-level radioactive waste (LLRW)? Among the results of my calculations, I found that although EPA estimates for annual PCC disposal are 20% larger than industry statistics, these latter values appear to be closer to reality. Second, EPA appears to have significantly underestimated historical PCC disposal: my projections indicate that EPA’s maximum estimate for the quantity of fly ash landfilled within the past 90 years was likely met by production in the last 30 years alone, if not less. Finally, my analysis indicates that while PCCs may potentially meet the criteria for reclassification as low-level radioactive waste by NRC, the cost of such regulation would be many times that of the EPA June proposed disposal rule ($220-302 billion for PCCs disposed in 2008 alone, versus $1.47 billion per year for the Subtitle C option and $236-587 million for Subtitle D regulatory options).
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