Overcoming limitations of modelling rare species by using ensembles of small models

1. Species distribution models (SDMs) have become a standard tool in ecology and applied conservation biology. Modelling rare and threatened species is particularly important for conservation purposes. However, modelling rare species is difficult because the combination of few occurrences and many predictor variables easily leads to model overfitting. A new strategy using ensembles of small models was recently developed in an attempt to overcome this limitation of rare species modelling and has been tested successfully for only a single species so far. Here, we aim to test the approach more comprehensively on a large number of species including a transferability assessment. 2. For each species numerous small (here bivariate) models were calibrated, evaluated and averaged to an ensemble weighted by AUC scores. These 'ensembles of small models' (ESMs) were compared to standard Species Distribution Models (SDMs) using three commonly used modelling techniques (GLM, GBM, Maxent) and their ensemble prediction. We tested 107 rare and under-sampled plant species of conservation concern in Switzerland. 3. We show that ESMs performed significantly better than standard SDMs. The rarer the species, the more pronounced the effects were. ESMs were also superior to standard SDMs and their ensemble when they were independently evaluated using a transferability assessment. 4. By averaging simple small models to an ensemble, ESMs avoid overfitting without losing explanatory power through reducing the number of predictor variables. They further improve the reliability of species distribution models, especially for rare species, and thus help to overcome limitations of modelling rare species.

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes.

Background: Information about the composition of regulatory regions is of great value for designing experiments to functionally characterize gene expression. The multiplicity of available applications to predict transcription factor binding sites in a particular locus contrasts with the substantial computational expertise that is demanded to manipulate them, which may constitute a potential barrier for the experimental community. Results: CBS (Conserved regulatory Binding Sites, http://compfly.bio.ub.es/CBS) is a public platform of evolutionarily conserved binding sites and enhancers predicted in multiple Drosophila genomes that is furnished with published chromatin signatures associated to transcriptionally active regions and other experimental sources of information. The rapid access to this novel body of knowledge through a user-friendly web interface enables non-expert users to identify the binding sequences available for any particular gene, transcription factor, or genome region. Conclusions: The CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings in Drosophila.

New kernel functions and learning methods for text and data mining

Recent advances in machine learning methods enable increasingly the automatic construction of various types of computer assisted methods that have been difficult or laborious to program by human experts. The tasks for which this kind of tools are needed arise in many areas, here especially in the fields of bioinformatics and natural language processing. The machine learning methods may not work satisfactorily if they are not appropriately tailored to the task in question. However, their learning performance can often be improved by taking advantage of deeper insight of the application domain or the learning problem at hand. This thesis considers developing kernel-based learning algorithms incorporating this kind of prior knowledge of the task in question in an advantageous way. Moreover, computationally efficient algorithms for training the learning machines for specific tasks are presented. In the context of kernel-based learning methods, the incorporation of prior knowledge is often done by designing appropriate kernel functions. Another well-known way is to develop cost functions that fit to the task under consideration. For disambiguation tasks in natural language, we develop kernel functions that take account of the positional information and the mutual similarities of words. It is shown that the use of this information significantly improves the disambiguation performance of the learning machine. Further, we design a new cost function that is better suitable for the task of information retrieval and for more general ranking problems than the cost functions designed for regression and classification. We also consider other applications of the kernel-based learning algorithms such as text categorization, and pattern recognition in differential display. We develop computationally efficient algorithms for training the considered learning machines with the proposed kernel functions. We also design a fast cross-validation algorithm for regularized least-squares type of learning algorithm. Further, an efficient version of the regularized least-squares algorithm that can be used together with the new cost function for preference learning and ranking tasks is proposed. In summary, we demonstrate that the incorporation of prior knowledge is possible and beneficial, and novel advanced kernels and cost functions can be used in algorithms efficiently.

Reuse of information for selection of methods and operating conditions for drying of pharmaceutical materials

Drying is a major step in the manufacturing process in pharmaceutical industries, and the selection of dryer and operating conditions are sometimes a bottleneck. In spite of difficulties, the bottlenecks are taken care of with utmost care due to good manufacturing practices (GMP) and industries' image in the global market. The purpose of this work is to research the use of existing knowledge for the selection of dryer and its operating conditions for drying of pharmaceutical materials with the help of methods like case-based reasoning and decision trees to reduce time and expenditure for research. The work consisted of two major parts as follows: Literature survey on the theories of spray dying, case-based reasoning and decision trees; working part includes data acquisition and testing of the models based on existing and upgraded data. Testing resulted in a combination of two models, case-based reasoning and decision trees, leading to more specific results when compared to conventional methods.

Implementing Agile Software Development Methods in a Small Organization

Currently there is a vogue for Agile Software Development methods and many software development organizations have already implemented or they are planning to implement agile methods. Objective of this thesis is to define how agile software development methods are implemented in a small organization. Agile methods covered in this thesis are Scrum and XP. From both methods the key practices are analysed and compared to waterfall method. This thesis also defines implementation strategy and actions how agile methods are implemented in a small organization. In practice organization must prepare well and all needed meters are defined before the implementation starts. In this work three different sample projects are introduced where agile methods were implemented. Experiences from these projects were encouraging although sample set of projects were too small to get trustworthy results.

Premières évidences de la validité de l'échelle de désengagement moral pour des actes discriminatoires (Initial evidence of the validity of a scale on moral disengagement in discriminatory behavior)

De nombreuses études ont mis en évidence le fait que les individus étaient prêts à commettre des actes discriminatoires pour autant qu'ils puissent les justifier (Crandall & Eshleman, 2003). Nous proposons de contribuer à la compréhension de ce phénomène grâce au concept de désengagement moral pour des actes discriminatoires (DMD). Nous définissons le désengagement moral comme le fait de justifier ses propres actes immoraux de manière à les rendre acceptable. Ce concept trouve ses origines dans les travaux de Bandura et al. (1996) portant sur les comportements agressifs chez des enfants. Il se compose de huit mécanismes (p.ex. le déplacement de responsabilité). Notre recherche dépasse le cadre théorique développé par Bandura et al. pour inscrire le désengagement moral dans le champ de la discrimination intergroupe. De plus, en conceptualisant le désengagement moral comme une différence individuelle, nous proposons également de présenter les premières étapes du développement d'une échelle permettant de mesurer le DMD. L'échelle de DMD a été développée en trois étapes en suivant la procédure proposée par Hinkin (1998). Tout d'abord, une liste de 72 items a été générée suivant une méthode déductive. Puis, suite à une étude (n = 13) portant sur la cohérence des items vis-à-vis du concept et de ses mécanismes, cette liste a été réduite à 40 items (5 par mécanisme). Enfin, 118 étudiants universitaires ont participé à une étude dans le but de mener des analyses factorielles (exploratoire et confirmatoire), ainsi que de tester les validités convergente, divergente et prédictive de l'échelle. La première partie de cette étude se composait de différentes échelles (p.ex. mesure de personnalité, préjugés anti-immigrés, etc.). La seconde partie de l'étude était une expérience portant sur l'évaluation d'idées de méthodes de sélection (discriminatoire versus méritocratique) des étudiants suisses et étrangers à l'université, ayant pour but de réduire la surpopulation dans les salles de cours. Les résultats obtenus sont prometteurs pour le développement de l'échelle, autant du point de vue de sa structure (p.ex. α = .82) que de sa validité. Par exemple, plus le niveau de DMD des participants était élevé, plus ils étaient favorables à une méthode de sélection discriminatoire des étudiants à l'université. L'ensemble des résultats sera présenté durant la conférence. Nous discuterons également des potentielles contributions de cette échelle pour de futurs projets de recherche. Référence : Bandura, A., Barbaranelli, C., Caprara, G. V., & Pastorelli, C. (1996). Mechanisms of moral disengagement of the exercise of moral agency. Journal of Personality and Social Psychology, 71 (2), 364-374. Crandall, C. S., & Eshleman, A. (2003). The Justification-suppression model of the expression and experience of prejudice. Psychological Bulletin, 129 (3), 414-446. Hinkin, T. R. (1998). A brief tutorial on the development of measures for use un survey questionnaires. Organizational Research Methods, 1 (1), 104.121.

Use of Statistical Methods in Demand Planning

In a very volatile industry of high technology it is of utmost importance to accurately forecast customers’ demand. However, statistical forecasting of sales, especially in heavily competitive electronics product business, has always been a challenging task due to very high variation in demand and very short product life cycles of products. The purpose of this thesis is to validate if statistical methods can be applied to forecasting sales of short life cycle electronics products and provide a feasible framework for implementing statistical forecasting in the environment of the case company. Two different approaches have been developed for forecasting on short and medium term and long term horizons. Both models are based on decomposition models, but differ in interpretation of the model residuals. For long term horizons residuals are assumed to represent white noise, whereas for short and medium term forecasting horizon residuals are modeled using statistical forecasting methods. Implementation of both approaches is performed in Matlab. Modeling results have shown that different markets exhibit different demand patterns and therefore different analytical approaches are appropriate for modeling demand in these markets. Moreover, the outcomes of modeling imply that statistical forecasting can not be handled separately from judgmental forecasting, but should be perceived only as a basis for judgmental forecasting activities. Based on modeling results recommendations for further deployment of statistical methods in sales forecasting of the case company are developed.

A comparison of three established age estimation methods on an adult Spanish sample.

Most current methods for adult skeletal age-at-death estimation are based on American samples comprising individuals of European and African ancestry. Our limited understanding of population variability hampers our efforts to apply these techniques to various skeletal populations around the world, especially in global forensic contexts. Further, documented skeletal samples are rare, limiting our ability to test our techniques. The objective of this paper is to test three pelvic macroscopic methods (1-Suchey-Brooks; 2- Lovejoy; 3- Buckberry and Chamberlain) on a documented modern Spanish sample. These methods were selected because they are popular among Spanish anthropologists and because they never have been tested in a Spanish sample. The study sample consists of 80 individuals (55 ♂ and 25 ♀) of known sex and age from the Valladolid collection. Results indicate that in all three methods, levels of bias and inaccuracy increase with age. The Lovejoy method performs poorly (27%) compared with Suchey-Brooks (71%) and Buckberry and Chamberlain (86%). However, the levels of correlation between phases and chronological ages are low and comparable in the three methods (< 0.395). The apparent accuracy of the Suchey-Brooks and Buckberry and Chamberlain methods is largely based on the broad width of the methods" estimated intervals. This study suggests that before systematic application of these three methodologies in Spanish populations, further statistical modeling and research into the co-variance of chronological age with morphological change is necessary. Future methods should be developed specific to various world populations, and should allow for both precision and flexibility in age estimation.

Mieux comprendre le syndrome douloureux fémoro-patellaire... pour mieux le traiter [Patellofemoral pain syndrome: understand better in order to treat better].

Le syndrome douloureux fémoro-patellaire (SDFP) est l'une des causes les plus fréquentes de douleur antérieure du genou chez l'adolescent et l'adulte. De par son étiologie complexe, multifactorielle et encore mal comprise, sa prise en charge est un important challenge pour le praticien. Le diagnostic se fait principalement sur l'anamnèse et l'examen clinique du genou mais aussi de l'ensemble du membre inférieur, pouvant parfois nécessiter la réalisation d'une imagerie. Le traitement est dans la grande majorité des cas conservateur, principalement axé sur la rééducation avec de la physiothérapie ciblée et personnalisée. Le traitement chirurgical est réservé aux cas présentant une anomalie structurelle causale. Patellofemoral pain syndrome (PFPS) is one of the most frequent cause of anterior knee pain in adolescents and adults. Due to its complex etiology, which is multifactorial and still poorly understood, its management is a major challenge for the practitioner. The diagnosis is made primarily on the history and clinical examination of the knee, but also of the entire lower limb, which may sometimes require the completion of imaging. The treatment is mostly conservative, focussing on rehabilitation with targeted and personalized therapy. Surgical treatment is reserved for cases with a causal structural lesion.

The Coordinated Radio and Infrared Survey for High-mass Star Formation. II. Source Catalog

The CORNISH project is the highest resolution radio continuum survey of the Galactic plane to date. It is the 5 GHz radio continuum part of a series of multi-wavelength surveys that focus on the northern GLIMPSE region (10° < l < 65°), observed by the Spitzer satellite in the mid-infrared. Observations with the Very Large Array in B and BnA configurations have yielded a 1.''5 resolution Stokes I map with a root mean square noise level better than 0.4 mJy beam 1. Here we describe the data-processing methods and data characteristics, and present a new, uniform catalog of compact radio emission. This includes an implementation of automatic deconvolution that provides much more reliable imaging than standard CLEANing. A rigorous investigation of the noise characteristics and reliability of source detection has been carried out. We show that the survey is optimized to detect emission on size scales up to 14'' and for unresolved sources the catalog is more than 90% complete at a flux density of 3.9 mJy. We have detected 3062 sources above a 7σ detection limit and present their ensemble properties. The catalog is highly reliable away from regions containing poorly sampled extended emission, which comprise less than 2% of the survey area. Imaging problems have been mitigated by down-weighting the shortest spacings and potential artifacts flagged via a rigorous manual inspection with reference to the Spitzer infrared data. We present images of the most common source types found: H II regions, planetary nebulae, and radio galaxies. The CORNISH data and catalog are available online at http://cornish.leeds.ac.uk.

A test of Suchey-Brooks (pubic symphysis) and Buckberry-Chamberlain (auricular surface) methods on an identified Spanish sample: paleodemographic implications

Forensic Anthropology and Bioarchaeology studies depend critically on the accuracy and reliability of age-estimation techniques. In this study we have evaluated two age-estimation methods for adults based on the pubic symphysis (Suchey-Brooks) and the auricular surface (Buckberry-Chamberlain) in a current sample of 139 individuals (67 women and 72 men) from Madrid in order to verify the accuracy of both methods applied to a sample of innominate bones from the central Iberian Peninsula. Based on the overall results of this study, the Buckberry-Chamberlain method seems to be the method that provides better estimates in terms of accuracy (percentage of hits) and absolute difference to the chronological age taking into account the total sample. The percentage of hits and mean absolute difference of the Buckberry-Chamberlain and Suchey-Brooks methods are 97.3% and 11.24 years, and 85.7% and 14.38 years, respectively. However, this apparently greater applicability of the Buckberry-Chamberlain method is mainly due to the broad age ranges provided. Results indicated that Suchey-Brooks method is more appropriate for populations with a majority of young individuals, whereas Buckberry-Chamberlain method is recommended for populations with a higher percentage of individuals in the range 60-70 years. These different age estimation methodologies significantly influence the resulting demographic profile, consequently affecting the biological characteristics reconstruction of the samples in which they are applied.

Fast and economic immobilization methods described for non-commercial Pseudomonas lipases

There is an increasing interest to seek new enzyme preparations for the development of new products derived from bioprocesses to obtain alternative bio-based materials. In this context, four non-commercial lipases from Pseudomonas species were prepared, immobilized on different low-cost supports, and examined for potential biotechnological applications. Results: To reduce costs of eventual scaling-up, the new lipases were obtained directly from crude cell extracts or from growth culture supernatants, and immobilized by simple adsorption on Accurel EP100, Accurel MP1000 and Celite (R) 545. The enzymes evaluated were LipA and LipC from Pseudomonas sp. 42A2, a thermostable mutant of LipC, and LipI. 3 from Pseudomonas CR611, which were produced in either homologous or heterologous hosts. Best immobilization results were obtained on Accurel EP100 for LipA and on Accurel MP1000 for LipC and its thermostable variant. Lip I. 3, requiring a refolding step, was poorly immobilized on all supports tested ( best results for Accurel MP1000). To test the behavior of immobilized lipases, they were assayed in triolein transesterification, where the best results were observed for lipases immobilized on Accurel MP1000. Conclusions: The suggested protocol does not require protein purification and uses crude enzymes immobilized by a fast adsorption technique on low-cost supports, which makes the method suitable for an eventual scaling up aimed at biotechnological applications. Therefore, a fast, simple and economic method for lipase preparation and immobilization has been set up. The low price of the supports tested and the simplicity of the procedure, skipping the tedious and expensive purification steps, will contribute to cost reduction in biotechnological lipase-catalyzed processes.

Diagnostic methods and treatment options for focal cortical dysplasia.

Our inability to adequately treat many patients with refractory epilepsy caused by focal cortical dysplasia (FCD), surgical inaccessibility and failures are significant clinical drawbacks. The targeting of physiologic features of epileptogenesis in FCD and colocalizing functionality has enhanced completeness of surgical resection, the main determinant of outcome. Electroencephalography (EEG)-functional magnetic resonance imaging (fMRI) and magnetoencephalography are helpful in guiding electrode implantation and surgical treatment, and high-frequency oscillations help defining the extent of the epileptogenic dysplasia. Ultra high-field MRI has a role in understanding the laminar organization of the cortex, and fluorodeoxyglucose-positron emission tomography (FDG-PET) is highly sensitive for detecting FCD in MRI-negative cases. Multimodal imaging is clinically valuable, either by improving the rate of postoperative seizure freedom or by reducing postoperative deficits. However, there is no level 1 evidence that it improves outcomes. Proof for a specific effect of antiepileptic drugs (AEDs) in FCD is lacking. Pathogenic mutations recently described in mammalian target of rapamycin (mTOR) genes in FCD have yielded important insights into novel treatment options with mTOR inhibitors, which might represent an example of personalized treatment of epilepsy based on the known mechanisms of disease. The ketogenic diet (KD) has been demonstrated to be particularly effective in children with epilepsy caused by structural abnormalities, especially FCD. It attenuates epigenetic chromatin modifications, a master regulator for gene expression and functional adaptation of the cell, thereby modifying disease progression. This could imply lasting benefit of dietary manipulation. Neurostimulation techniques have produced variable clinical outcomes in FCD. In widespread dysplasias, vagus nerve stimulation (VNS) has achieved responder rates >50%; however, the efficacy of noninvasive cranial nerve stimulation modalities such as transcutaneous VNS (tVNS) and noninvasive (nVNS) requires further study. Although review of current strategies underscores the serious shortcomings of treatment-resistant cases, initial evidence from novel approaches suggests that future success is possible.