Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

Affiliation: Département de Biochimie, Université de Montréal

Demografía de la metapoblación y estructura horizontal de aedes aegypti (L.) en el área metropolitana de Monterrey

Tesis (Doctorado en Ciencias Biológicas con Especialidad en Entomología) U.A.N.L

Desarrollo, optimización e integración de tecnologías sustentables a base de un biorreactor empacado de flujo ascendente y un humedal artificial de flujo horizontal sub-superficial para el tratamiento de agua contaminada con cromo y plomo.

Tesis (Doctor en Ciencias con Especialidad en Biotecnología) UANL, 2013

Étude des étoiles de la branche horizontale extrême par l'astérosismologie

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Développement d’un algorithme de branch-and-price-and-cut pour le problème de conception de réseau avec coûts fixes et capacités

De nombreux problèmes en transport et en logistique peuvent être formulés comme des modèles de conception de réseau. Ils requièrent généralement de transporter des produits, des passagers ou encore des données dans un réseau afin de satisfaire une certaine demande tout en minimisant les coûts. Dans ce mémoire, nous nous intéressons au problème de conception de réseau avec coûts fixes et capacités. Ce problème consiste à ouvrir un sous-ensemble des liens dans un réseau afin de satisfaire la demande, tout en respectant les contraintes de capacités sur les liens. L'objectif est de minimiser les coûts fixes associés à l'ouverture des liens et les coûts de transport des produits. Nous présentons une méthode exacte pour résoudre ce problème basée sur des techniques utilisées en programmation linéaire en nombres entiers. Notre méthode est une variante de l'algorithme de branch-and-bound, appelée branch-and-price-and-cut, dans laquelle nous exploitons à la fois la génération de colonnes et de coupes pour la résolution d'instances de grande taille, en particulier, celles ayant un grand nombre de produits. En nous comparant à CPLEX, actuellement l'un des meilleurs logiciels d'optimisation mathématique, notre méthode est compétitive sur les instances de taille moyenne et supérieure sur les instances de grande taille ayant un grand nombre de produits, et ce, même si elle n'utilise qu'un seul type d'inégalités valides.

L'algorithme de Branch and Price and Cut pour le problème de conception de réseaux avec coûts fixes et sans capacité

Le problème de conception de réseaux est un problème qui a été beaucoup étudié dans le domaine de la recherche opérationnelle pour ses caractéristiques, et ses applications dans des nombreux domaines tels que le transport, les communications, et la logistique. Nous nous intéressons en particulier dans ce mémoire à résoudre le problème de conception de réseaux avec coûts fixes et sans capacité, en satisfaisant les demandes de tous les produits tout en minimisant la somme des coûts de transport de ces produits et des coûts fixes de conception du réseau. Ce problème se modélise généralement sous la forme d’un programme linéaire en nombres entiers incluant des variables continues. Pour le résoudre, nous avons appliqué la méthode exacte de Branch-and-Bound basée sur une relaxation linéaire du problème avec un critère d’arrêt, tout en exploitant les méthodes de génération de colonnes et de génération de coupes. Nous avons testé la méthode de Branch-and-Price-and-Cut sur 156 instances divisées en cinq groupes de différentes tailles, et nous l’avons comparée à Cplex, l’un des meilleurs solveurs d’optimisation mathématique, ainsi qu’à la méthode de Branch-and- Cut. Notre méthode est compétitive et plus performante sur les instances de grande taille ayant un grand nombre de produits.

Studies on the Vertical Structure of Horizontal Wind Variability in the Surface Boundary Layer Over Sriharikota

The present study on the vertical structure of horizontal wind variability in the surface boundary layer over Sriharikota. Based on clock wind speed and direction measuring meteorological tower facility from seven levels in the 100 m layer. The study on wind variability and elliptical approximation of wind hodographs investigated for this tropical coastal station established that Sriharikota is of meso-scale weather entity. Wind variability ratio increases from lower levels to upper levels. In South West monsoon months the station is of high ratio values and it gets affected with meso-scale weather features like thunderstorms. Average total shears are observed greater values than scalar shears. Scalar shears are high in the lowest shear levels compared to upper levels. Semi diurnal types of oscillation in average total shears are found in south west monsoon months. During cyclonic storm passage it is observed that there can be significant difference in mean wind speed from 10 m to 100 m level, but it is not so for peak wind speeds. The variations in wind variability ratio in different months is clearly depicted its strong link to define meso-scale or synoptic –scale forcing domination for this station. Meso-scale forcing is characterized by diurnal wind variability and synoptic- scale forcing by interdiurnal wind variability.

Techniques for Enhancing Wind Energy Generation - A CFD Based Multibody Dynamics Approach in Horizontal Axis Wind Turbines

Wind energy has emerged as a major sustainable source of energy.The efficiency of wind power generation by wind mills has improved a lot during the last three decades.There is still further scope for maximising the conversion of wind energy into mechanical energy.In this context,the wind turbine rotor dynamics has great significance.The present work aims at a comprehensive study of the Horizontal Axis Wind Turbine (HAWT) aerodynamics by numerically solving the fluid dynamic equations with the help of a finite-volume Navier-Stokes CFD solver.As a more general goal,the study aims at providing the capabilities of modern numerical techniques for the complex fluid dynamic problems of HAWT.The main purpose is hence to maximize the physics of power extraction by wind turbines.This research demonstrates the potential of an incompressible Navier-Stokes CFD method for the aerodynamic power performance analysis of horizontal axis wind turbine.The National Renewable Energy Laboratory USA-NREL (Technical Report NREL/Cp-500-28589) had carried out an experimental work aimed at the real time performance prediction of horizontal axis wind turbine.In addition to a comparison between the results reported by NREL made and CFD simulations,comparisons are made for the local flow angle at several stations ahead of the wind turbine blades.The comparison has shown that fairly good predictions can be made for pressure distribution and torque.Subsequently, the wind-field effects on the blade aerodynamics,as well as the blade/tower interaction,were investigated.The selected case corresponded to a 12.5 m/s up-wind HAWT at zero degree of yaw angle and a rotational speed of 25 rpm.The results obtained suggest that the present can cope well with the flows encountered around wind turbines.The areodynamic performance of the turbine and the flow details near and off the turbine blades and tower can be analysed using theses results.The aerodynamic performance of airfoils differs from one another.The performance mainly depends on co-efficient of performnace,co-efficient of lift,co-efficient of drag, velocity of fluid and angle of attack.This study shows that the velocity is not constant for all angles of attack of different airfoils.The performance parameters are calculated analytically and are compared with the standardized performance tests.For different angles of ,the velocity stall is determined for the better performance of a system with respect to velocity.The research addresses the effect of surface roughness factor on the blade surface at various sections.The numerical results were found to be in agreement with the experimental data.A relative advantage of the theoretical aerofoil design method is that it allows many different concepts to be explored economically.Such efforts are generally impractical in wind tunnels because of time and money constraints.Thus, the need for a theoretical aerofoil design method is threefold:first for the design of aerofoil that fall outside the range of applicability of existing calalogs:second,for the design of aerofoil that more exactly match the requirements of the intended application:and third,for the economic exploration of many aerofoil concepts.From the results obtained for the different aerofoils,the velocity is not constant for all angles of attack.The results obtained for the aerofoil mainly depend on angle of attack and velocity.The vortex generator technique was meticulously studies with the formulation of the specification for the right angle shaped vortex generators-VG.The results were validated in accordance with the primary analysis phase.The results were found to be in good agreement with the power curve.The introduction of correct size VGs at appropriate locations over the blades of the selected HAWT was found to increase the power generation by about 4%

Power Profile of Effective Managers: An Exploration among the Branch Managers of a Commercial Bank in Kerala

Managers are central to any fuction in a complex and developed society. Their talents are reckoned to be cardinal in developed economies and a basic yearning of all developing economies.In order to survive and produce results in a turbulent and transient environment, the task is to understand the nature of factors contributing to managerial effectiveness. This study is an attempt towards this core issue of the present from a different perspective. This study tries to focus attention on a group of managers functioning in the field of banking, a core sector in the country's economy. The gamut of economic activities in Kerala being predominantly service-oriented, importance of commercial banking is almost indisputable. Though economists would argue that the disproportionate development of service sector is anomalous when viewed against the hazy scenarios in the primary and secondary sectors of the state’s economy, the extent and pace of growth in the banking sector has had its dole meted out by ambitious and productive managers fiinctioning in the field. Researcher’s attempt here is to thresh the grain and chaff among bank managers in terms of their effectiveness and to account for the variations in the light of their ability to affect the thoughts and actions of their subordinates. To put it succinctly, the attempt herein is to explain the effectiveness of bank managers in the light of their ‘Power Profile’ taken to be comprising Power Differentials, Power Bases, their Visibility and Credibility in the organisation and, the Power Styles typically used by them for influencing subordinates.

Maximum mass of neutron stars

We determine the structure of neutron stars within a Brueckner-Hartree-Fock approach based on realistic nucleon-nucleon, nucleon-hyperon, and hyperon-hyperon interactions. Our results indicate rather low maximum masses below 1.4 solar masses. This feature is insensitive to the nucleonic part of the EOS due to a strong compensation mechanism caused by the appearance of hyperons and represents thus strong evidence for the presence of nonbaryonic "quark" matter in the interior of heavy stars.

Studies on the horizontal and vertical distribution of clouds and their impact on energetics of the Atmosphere over the Indian Region

Motivation for the present study is to improve the scienti c understanding on the prominent gap areas in the average three-dimensional distribution of clouds and their impact on the energetics of the earth-atmosphere system. This study is focused on the Indian subcontinent and the surrounding oceans bound within the latitude-longitude bands of 30 S to 30 N and 30 E to 110 E. Main objectives of this study are to : (i) estimate the monthly and seasonal mean vertical distributions of clouds and their spatial variations (which provide the monthly and seasonal mean 3-dimensional distributions of clouds) using multi-year satellite data and investigate their association with the general circulation of the atmosphere, (ii) investigate the characteristics of the `pool of inhibited cloudiness' that appear over the southwest Bay of Bengal during the Asian summer monsoon season (revealed by the 3-dimensional distribution of clouds) and identify the potential mechanisms for its genesis, (iii) investigate the role of SST and atmospheric thermo-dynamical parameters in regulating the vertical development and distribution of clouds, (iv) investigate the vertical distribution of tropical cirrus clouds and their descending nature using lidar observations at Thiruvananthapuram (8.5 N, 77 E), a tropical coastal station at the southwest Peninsular India, and (v) assessment of the impact of clouds on the energetics of the earth-atmosphere system, by estimating the regional seasonal mean cloud radiative forcing at top-of-the-atmosphere (TOA) and latent heating of the atmosphere by precipitating clouds using satellite data

Study on period search methods of variable stars: Application to ASAS and CRTS databases

Study on variable stars is an important topic of modern astrophysics. After the invention of powerful telescopes and high resolving powered CCD’s, the variable star data is accumulating in the order of peta-bytes. The huge amount of data need lot of automated methods as well as human experts. This thesis is devoted to the data analysis on variable star’s astronomical time series data and hence belong to the inter-disciplinary topic, Astrostatistics. For an observer on earth, stars that have a change in apparent brightness over time are called variable stars. The variation in brightness may be regular (periodic), quasi periodic (semi-periodic) or irregular manner (aperiodic) and are caused by various reasons. In some cases, the variation is due to some internal thermo-nuclear processes, which are generally known as intrinsic vari- ables and in some other cases, it is due to some external processes, like eclipse or rotation, which are known as extrinsic variables. Intrinsic variables can be further grouped into pulsating variables, eruptive variables and flare stars. Extrinsic variables are grouped into eclipsing binary stars and chromospheri- cal stars. Pulsating variables can again classified into Cepheid, RR Lyrae, RV Tauri, Delta Scuti, Mira etc. The eruptive or cataclysmic variables are novae, supernovae, etc., which rarely occurs and are not periodic phenomena. Most of the other variations are periodic in nature. Variable stars can be observed through many ways such as photometry, spectrophotometry and spectroscopy. The sequence of photometric observa- xiv tions on variable stars produces time series data, which contains time, magni- tude and error. The plot between variable star’s apparent magnitude and time are known as light curve. If the time series data is folded on a period, the plot between apparent magnitude and phase is known as phased light curve. The unique shape of phased light curve is a characteristic of each type of variable star. One way to identify the type of variable star and to classify them is by visually looking at the phased light curve by an expert. For last several years, automated algorithms are used to classify a group of variable stars, with the help of computers. Research on variable stars can be divided into different stages like observa- tion, data reduction, data analysis, modeling and classification. The modeling on variable stars helps to determine the short-term and long-term behaviour and to construct theoretical models (for eg:- Wilson-Devinney model for eclips- ing binaries) and to derive stellar properties like mass, radius, luminosity, tem- perature, internal and external structure, chemical composition and evolution. The classification requires the determination of the basic parameters like pe- riod, amplitude and phase and also some other derived parameters. Out of these, period is the most important parameter since the wrong periods can lead to sparse light curves and misleading information. Time series analysis is a method of applying mathematical and statistical tests to data, to quantify the variation, understand the nature of time-varying phenomena, to gain physical understanding of the system and to predict future behavior of the system. Astronomical time series usually suffer from unevenly spaced time instants, varying error conditions and possibility of big gaps. This is due to daily varying daylight and the weather conditions for ground based observations and observations from space may suffer from the impact of cosmic ray particles. Many large scale astronomical surveys such as MACHO, OGLE, EROS, xv ROTSE, PLANET, Hipparcos, MISAO, NSVS, ASAS, Pan-STARRS, Ke- pler,ESA, Gaia, LSST, CRTS provide variable star’s time series data, even though their primary intention is not variable star observation. Center for Astrostatistics, Pennsylvania State University is established to help the astro- nomical community with the aid of statistical tools for harvesting and analysing archival data. Most of these surveys releases the data to the public for further analysis. There exist many period search algorithms through astronomical time se- ries analysis, which can be classified into parametric (assume some underlying distribution for data) and non-parametric (do not assume any statistical model like Gaussian etc.,) methods. Many of the parametric methods are based on variations of discrete Fourier transforms like Generalised Lomb-Scargle peri- odogram (GLSP) by Zechmeister(2009), Significant Spectrum (SigSpec) by Reegen(2007) etc. Non-parametric methods include Phase Dispersion Minimi- sation (PDM) by Stellingwerf(1978) and Cubic spline method by Akerlof(1994) etc. Even though most of the methods can be brought under automation, any of the method stated above could not fully recover the true periods. The wrong detection of period can be due to several reasons such as power leakage to other frequencies which is due to finite total interval, finite sampling interval and finite amount of data. Another problem is aliasing, which is due to the influence of regular sampling. Also spurious periods appear due to long gaps and power flow to harmonic frequencies is an inherent problem of Fourier methods. Hence obtaining the exact period of variable star from it’s time series data is still a difficult problem, in case of huge databases, when subjected to automation. As Matthew Templeton, AAVSO, states “Variable star data analysis is not always straightforward; large-scale, automated analysis design is non-trivial”. Derekas et al. 2007, Deb et.al. 2010 states “The processing of xvi huge amount of data in these databases is quite challenging, even when looking at seemingly small issues such as period determination and classification”. It will be beneficial for the variable star astronomical community, if basic parameters, such as period, amplitude and phase are obtained more accurately, when huge time series databases are subjected to automation. In the present thesis work, the theories of four popular period search methods are studied, the strength and weakness of these methods are evaluated by applying it on two survey databases and finally a modified form of cubic spline method is intro- duced to confirm the exact period of variable star. For the classification of new variable stars discovered and entering them in the “General Catalogue of Vari- able Stars” or other databases like “Variable Star Index“, the characteristics of the variability has to be quantified in term of variable star parameters.

Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.

Horizontal nutrient fluxes and production efficiencies in urban and peri-urban crop and livestock husbandry of Niamey, Niger

Urban and peri-urban agriculture (UPA) increasingly supplies food and non-food values to the rapidly growing West African cities. However, little is known about the resource use efficiencies in West African small-scale UPA crop and livestock production systems, and about the benefits that urban producers and retailers obtain from the cultivation and sale of UPA products. To contribute to filling this gap of knowledge, the studies comprising this doctoral thesis determined nutrient use efficiencies in representative urban crop and livestock production system in Niamey, Niger, and investigated potential health risks for consumers. Also assessed was the economic efficiency of urban farming activities. The field study, which was conducted during November 2005 to January 2008, quantified management-related horizontal nutrient flows in 10 vegetable gardens, 9 millet fields and 13 cattle and small ruminant production units. These farms, selected on the basis of a preceding study, represented the diversity of UPA crop and livestock production systems in Niamey. Based on the management intensity, the market orientation and especially the nutrient input to individual gardens and fields, these were categorized as high or low input systems. In the livestock study, high and low input cattle and small ruminant units were differentiated based on the amounts of total feed dry matter offered daily to the animals at the homestead. Additionally, economic returns to gardeners and market retailers cultivating and selling amaranth, lettuce, cabbage and tomato - four highly appreciated vegetables in Niamey were determined during a 6-months survey in forty gardens and five markets. For vegetable gardens and millet fields, significant differences in partial horizontal nutrient balances were determined for both management intensities. Per hectare, average annual partial balances for carbon (C), nitrogen (N), phosphorus (P) and potassium (K) amounted to 9936 kg C, 1133 kg N, 223 kg P and 312 kg K in high input vegetable gardens as opposed to 9580 kg C, 290 kg N, 125 kg P and 351 kg K in low input gardens. These surpluses were mainly explained by heavy use of mineral fertilizers and animal manure to which irrigation with nutrient rich wastewater added. In high input millet fields, annual surpluses of 259 kg C ha-1, 126 kg N ha-1, 20 kg P ha-1 and 0.4 kg K ha-1 were determined. Surpluses of 12 kg C ha-1, 17 kg N ha-1, and deficits of -3 kg P ha-1 and -3 kg K ha-1 were determined for low input millet fields. Here, carbon and nutrient inputs predominantly originated from livestock manure application through corralling of sheep, goats and cattle. In the livestock enterprises, N, P and K supplied by forages offered at the farm exceeded the animals’ requirements for maintenance and growth in high and low input sheep/goat as well as cattle units. The highest average growth rate determined in high input sheep/goat units was 104 g d-1 during the cool dry season, while a maximum average gain of 70 g d-1 was determined for low input sheep/goat units during the hot dry season. In low as well as in high input cattle units, animals lost weight during the hot dry season, and gained weight during the cool dry season. In all livestock units, conversion efficiencies for feeds offered at the homestead were rather poor, ranging from 13 to 42 kg dry matter (DM) per kg live weight gain (LWG) in cattle and from 16 to 43 kg DM kg-1 LWG in sheep/goats, pointing to a substantial waste of feeds and nutrients. The economic assessment of the production of four high value vegetables pointed to a low efficiency of N and P use in amaranth and lettuce production, causing low economic returns for these crops compared to tomato and cabbage to which inexpensive animal manure was applied. The net profit of market retailers depended on the type of vegetable marketed. In addition it depended on marketplace for amaranth and lettuce, and on season and marketplace for cabbage and tomato. Analysis of faecal pathogens in lettuce irrigated with river water and fertilized with animal manure indicated a substantial contamination by Salmonella spp. with 7.2 x 104 colony forming units (CFU) per 25 g of produce fresh matter, while counts of Escherichia coli averaged 3.9 x 104 CFU g-1. In lettuce irrigated with wastewater, Salmonella counts averaged 9.8 x 104 CFU 25 g-1 and E. coli counts were 0.6 x 104 CFU g-1; these values exceeded the tolerable contamination levels in vegetables of 10 CFU g-1 for E. coli and of 0 CFU 25 g-1 for Salmonella. Taken together, the results of this study indicate that Niamey’s UPA enterprises put environmental safety at risk since excess inputs of N, P and K to crop and livestock production units favour N volatilisation and groundwater pollution by nutrient leaching. However, more detailed studies are needed to corroborate these indications. Farmers’ revenues could be significantly increased if nutrient use efficiency in the different production (sub)systems was improved by better matching nutrient supply through fertilizers and feeds with the actual nutrient demands of plants and animals.