Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

A communication infrastructure to support knowledge level agents on the web

Agent Communication Languages (ACLs) have been developed to provide a way for agents to communicate with each other supporting cooperation in Multi-Agent Systems. In the past few years many ACLs have been proposed for Multi-Agent Systems, such as KQML and FIPA-ACL. The goal of these languages is to support high-level, human like communication among agents, exploiting Knowledge Level features rather than symbol level ones. Adopting these ACLs, and mainly the FIPA-ACL specifications, many agent platforms and prototypes have been developed. Despite these efforts, an important issue in the research on ACLs is still open and concerns how these languages should deal (at the Knowledge Level) with possible failures of agents. Indeed, the notion of Knowledge Level cannot be straightforwardly extended to a distributed framework such as MASs, because problems concerning communication and concurrency may arise when several Knowledge Level agents interact (for example deadlock or starvation). The main contribution of this Thesis is the design and the implementation of NOWHERE, a platform to support Knowledge Level Agents on the Web. NOWHERE exploits an advanced Agent Communication Language, FT-ACL, which provides high-level fault-tolerant communication primitives and satisfies a set of well defined Knowledge Level programming requirements. NOWHERE is well integrated with current technologies, for example providing full integration for Web services. Supporting different middleware used to send messages, it can be adapted to various scenarios. In this Thesis we present the design and the implementation of the architecture, together with a discussion of the most interesting details and a comparison with other emerging agent platforms. We also present several case studies where we discuss the benefits of programming agents using the NOWHERE architecture, comparing the results with other solutions. Finally, the complete source code of the basic examples can be found in appendix.

Self-Organizing Mechanisms for Task Allocation in a Knowledge-Based Economy

A prevalent claim is that we are in knowledge economy. When we talk about knowledge economy, we generally mean the concept of “Knowledge-based economy” indicating the use of knowledge and technologies to produce economic benefits. Hence knowledge is both tool and raw material (people’s skill) for producing some kind of product or service. In this kind of environment economic organization is undergoing several changes. For example authority relations are less important, legal and ownership-based definitions of the boundaries of the firm are becoming irrelevant and there are only few constraints on the set of coordination mechanisms. Hence what characterises a knowledge economy is the growing importance of human capital in productive processes (Foss, 2005) and the increasing knowledge intensity of jobs (Hodgson, 1999). Economic processes are also highly intertwined with social processes: they are likely to be informal and reciprocal rather than formal and negotiated. Another important point is also the problem of the division of labor: as economic activity becomes mainly intellectual and requires the integration of specific and idiosyncratic skills, the task of dividing the job and assigning it to the most appropriate individuals becomes arduous, a “supervisory problem” (Hogdson, 1999) emerges and traditional hierarchical control may result increasingly ineffective. Not only specificity of know how makes it awkward to monitor the execution of tasks, more importantly, top-down integration of skills may be difficult because ‘the nominal supervisors will not know the best way of doing the job – or even the precise purpose of the specialist job itself – and the worker will know better’ (Hogdson,1999). We, therefore, expect that the organization of the economic activity of specialists should be, at least partially, self-organized. The aim of this thesis is to bridge studies from computer science and in particular from Peer-to-Peer Networks (P2P) to organization theories. We think that the P2P paradigm well fits with organization problems related to all those situation in which a central authority is not possible. We believe that P2P Networks show a number of characteristics similar to firms working in a knowledge-based economy and hence that the methodology used for studying P2P Networks can be applied to organization studies. Three are the main characteristics we think P2P have in common with firms involved in knowledge economy: - Decentralization: in a pure P2P system every peer is an equal participant, there is no central authority governing the actions of the single peers; - Cost of ownership: P2P computing implies shared ownership reducing the cost of owing the systems and the content, and the cost of maintaining them; - Self-Organization: it refers to the process in a system leading to the emergence of global order within the system without the presence of another system dictating this order. These characteristics are present also in the kind of firm that we try to address and that’ why we have shifted the techniques we adopted for studies in computer science (Marcozzi et al., 2005; Hales et al., 2007 [39]) to management science.

Mathematical models of cognitive processes

The research activity carried out during the PhD course was focused on the development of mathematical models of some cognitive processes and their validation by means of data present in literature, with a double aim: i) to achieve a better interpretation and explanation of the great amount of data obtained on these processes from different methodologies (electrophysiological recordings on animals, neuropsychological, psychophysical and neuroimaging studies in humans), ii) to exploit model predictions and results to guide future research and experiments. In particular, the research activity has been focused on two different projects: 1) the first one concerns the development of neural oscillators networks, in order to investigate the mechanisms of synchronization of the neural oscillatory activity during cognitive processes, such as object recognition, memory, language, attention; 2) the second one concerns the mathematical modelling of multisensory integration processes (e.g. visual-acoustic), which occur in several cortical and subcortical regions (in particular in a subcortical structure named Superior Colliculus (SC)), and which are fundamental for orienting motor and attentive responses to external world stimuli. This activity has been realized in collaboration with the Center for Studies and Researches in Cognitive Neuroscience of the University of Bologna (in Cesena) and the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA). PART 1. Objects representation in a number of cognitive functions, like perception and recognition, foresees distribute processes in different cortical areas. One of the main neurophysiological question concerns how the correlation between these disparate areas is realized, in order to succeed in grouping together the characteristics of the same object (binding problem) and in maintaining segregated the properties belonging to different objects simultaneously present (segmentation problem). Different theories have been proposed to address these questions (Barlow, 1972). One of the most influential theory is the so called “assembly coding”, postulated by Singer (2003), according to which 1) an object is well described by a few fundamental properties, processing in different and distributed cortical areas; 2) the recognition of the object would be realized by means of the simultaneously activation of the cortical areas representing its different features; 3) groups of properties belonging to different objects would be kept separated in the time domain. In Chapter 1.1 and in Chapter 1.2 we present two neural network models for object recognition, based on the “assembly coding” hypothesis. These models are networks of Wilson-Cowan oscillators which exploit: i) two high-level “Gestalt Rules” (the similarity and previous knowledge rules), to realize the functional link between elements of different cortical areas representing properties of the same object (binding problem); 2) the synchronization of the neural oscillatory activity in the γ-band (30-100Hz), to segregate in time the representations of different objects simultaneously present (segmentation problem). These models are able to recognize and reconstruct multiple simultaneous external objects, even in difficult case (some wrong or lacking features, shared features, superimposed noise). In Chapter 1.3 the previous models are extended to realize a semantic memory, in which sensory-motor representations of objects are linked with words. To this aim, the network, previously developed, devoted to the representation of objects as a collection of sensory-motor features, is reciprocally linked with a second network devoted to the representation of words (lexical network) Synapses linking the two networks are trained via a time-dependent Hebbian rule, during a training period in which individual objects are presented together with the corresponding words. Simulation results demonstrate that, during the retrieval phase, the network can deal with the simultaneous presence of objects (from sensory-motor inputs) and words (from linguistic inputs), can correctly associate objects with words and segment objects even in the presence of incomplete information. Moreover, the network can realize some semantic links among words representing objects with some shared features. These results support the idea that semantic memory can be described as an integrated process, whose content is retrieved by the co-activation of different multimodal regions. In perspective, extended versions of this model may be used to test conceptual theories, and to provide a quantitative assessment of existing data (for instance concerning patients with neural deficits). PART 2. The ability of the brain to integrate information from different sensory channels is fundamental to perception of the external world (Stein et al, 1993). It is well documented that a number of extraprimary areas have neurons capable of such a task; one of the best known of these is the superior colliculus (SC). This midbrain structure receives auditory, visual and somatosensory inputs from different subcortical and cortical areas, and is involved in the control of orientation to external events (Wallace et al, 1993). SC neurons respond to each of these sensory inputs separately, but is also capable of integrating them (Stein et al, 1993) so that the response to the combined multisensory stimuli is greater than that to the individual component stimuli (enhancement). This enhancement is proportionately greater if the modality-specific paired stimuli are weaker (the principle of inverse effectiveness). Several studies have shown that the capability of SC neurons to engage in multisensory integration requires inputs from cortex; primarily the anterior ectosylvian sulcus (AES), but also the rostral lateral suprasylvian sulcus (rLS). If these cortical inputs are deactivated the response of SC neurons to cross-modal stimulation is no different from that evoked by the most effective of its individual component stimuli (Jiang et al 2001). This phenomenon can be better understood through mathematical models. The use of mathematical models and neural networks can place the mass of data that has been accumulated about this phenomenon and its underlying circuitry into a coherent theoretical structure. In Chapter 2.1 a simple neural network model of this structure is presented; this model is able to reproduce a large number of SC behaviours like multisensory enhancement, multisensory and unisensory depression, inverse effectiveness. In Chapter 2.2 this model was improved by incorporating more neurophysiological knowledge about the neural circuitry underlying SC multisensory integration, in order to suggest possible physiological mechanisms through which it is effected. This endeavour was realized in collaboration with Professor B.E. Stein and Doctor B. Rowland during the 6 months-period spent at the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA), within the Marco Polo Project. The model includes four distinct unisensory areas that are devoted to a topological representation of external stimuli. Two of them represent subregions of the AES (i.e., FAES, an auditory area, and AEV, a visual area) and send descending inputs to the ipsilateral SC; the other two represent subcortical areas (one auditory and one visual) projecting ascending inputs to the same SC. Different competitive mechanisms, realized by means of population of interneurons, are used in the model to reproduce the different behaviour of SC neurons in conditions of cortical activation and deactivation. The model, with a single set of parameters, is able to mimic the behaviour of SC multisensory neurons in response to very different stimulus conditions (multisensory enhancement, inverse effectiveness, within- and cross-modal suppression of spatially disparate stimuli), with cortex functional and cortex deactivated, and with a particular type of membrane receptors (NMDA receptors) active or inhibited. All these results agree with the data reported in Jiang et al. (2001) and in Binns and Salt (1996). The model suggests that non-linearities in neural responses and synaptic (excitatory and inhibitory) connections can explain the fundamental aspects of multisensory integration, and provides a biologically plausible hypothesis about the underlying circuitry.

Middleware principles and design for the integration of ubiquitos mobile services

Nowadays, in Ubiquitous computing scenarios users more and more require to exploit online contents and services by means of any device at hand, no matter their physical location, and by personalizing and tailoring content and service access to their own requirements. The coordinated provisioning of content tailored to user context and preferences, and the support for mobile multimodal and multichannel interactions are of paramount importance in providing users with a truly effective Ubiquitous support. However, so far the intrinsic heterogeneity and the lack of an integrated approach led to several either too vertical, or practically unusable proposals, thus resulting in poor and non-versatile support platforms for Ubiquitous computing. This work investigates and promotes design principles to help cope with these ever-changing and inherently dynamic scenarios. By following the outlined principles, we have designed and implemented a middleware support platform to support the provisioning of Ubiquitous mobile services and contents. To prove the viability of our approach, we have realized and stressed on top of our support platform a number of different, extremely complex and heterogeneous content and service provisioning scenarios. The encouraging results obtained are pushing our research work further, in order to provide a dynamic platform that is able to not only dynamically support novel Ubiquitous applicative scenarios by tailoring extremely diverse services and contents to heterogeneous user needs, but is also able to reconfigure and adapt itself in order to provide a truly optimized and tailored support for Ubiquitous service provisioning.

Neural basis of visual deficits recovery: visual residual functions and multisensory integration.

The ability of integrating into a unified percept sensory inputs deriving from different sensory modalities, but related to the same external event, is called multisensory integration and might represent an efficient mechanism of sensory compensation when a sensory modality is damaged by a cortical lesion. This hypothesis has been discussed in the present dissertation. Experiment 1 explored the role of superior colliculus (SC) in multisensory integration, testing patients with collicular lesions, patients with subcortical lesions not involving the SC and healthy control subjects in a multisensory task. The results revealed that patients with collicular lesions, paralleling the evidence of animal studies, demonstrated a loss of multisensory enhancement, in contrast with control subjects, providing the first lesional evidence in humans of the essential role of SC in mediating audio-visual integration. Experiment 2 investigated the role of cortex in mediating multisensory integrative effects, inducing virtual lesions by inhibitory theta-burst stimulation on temporo-parietal cortex, occipital cortex and posterior parietal cortex, demonstrating that only temporo-parietal cortex was causally involved in modulating the integration of audio-visual stimuli at the same spatial location. Given the involvement of the retino-colliculo-extrastriate pathway in mediating audio-visual integration, the functional sparing of this circuit in hemianopic patients is extremely relevant in the perspective of a multisensory-based approach to the recovery of unisensory defects. Experiment 3 demonstrated the spared functional activity of this circuit in a group of hemianopic patients, revealing the presence of implicit recognition of the fearful content of unseen visual stimuli (i.e. affective blindsight), an ability mediated by the retino-colliculo-extrastriate pathway and its connections with amygdala. Finally, Experiment 4 provided evidence that a systematic audio-visual stimulation is effective in inducing long-lasting clinical improvements in patients with visual field defect and revealed that the activity of the spared retino-colliculo-extrastriate pathway is responsible of the observed clinical amelioration, as suggested by the greater improvement observed in patients with cortical lesions limited to the occipital cortex, compared to patients with lesions extending to other cortical areas, found in tasks high demanding in terms of spatial orienting. Overall, the present results indicated that multisensory integration is mediated by the retino-colliculo-extrastriate pathway and that a systematic audio-visual stimulation, activating this spared neural circuit, is able to affect orientation towards the blind field in hemianopic patients and, therefore, might constitute an effective and innovative approach for the rehabilitation of unisensory visual impairments.

When the Practice of Theorizing Meets the Theorizing of Practice. Social Knowledge Making in Organization Science Academia and Managerial Communities

The aim of the present work is to contribute to a better understanding of the relation between organization theory and management practice. It is organized as a collection of two papers, a theoretical and conceptual contribution and an ethnographic study. The first paper is concerned with systematizing different literatures inside and outside the field of organization studies that deal with the theory-practice relation. After identifying a series of positions to the theory-practice debate and unfolding some of their implicit assumptions and limitations, a new position called entwinement is developed in order to overcome status quo through reconciliation and integration. Accordingly, the paper proposes to reconceptualize theory and practice as a circular iterative process of action and cognition, science and common-sense enacted in the real world both by organization scholars and practitioners according to purposes at hand. The second paper is the ethnographic study of an encounter between two groups of expert academics and practitioners occasioned by a one-year executive business master in an international business school. The research articulates a process view of the knowledge exchange between management academics and practitioners in particular and between individuals belonging to different communities of practice, in general, and emphasizes its dynamic, relational and transformative mechanisms. Findings show that when they are given the chance to interact, academics and practitioners set up local provisional relations that enable them to act as change intermediaries vis-a-vis each other’s worlds, without tying themselves irremediably to each other and to the scenarios they conjointly projected during the master’s experience. Finally, the study shows that provisional relations were accompanied by a recursive shift in knowledge modes. While interacting, academics passed from theory to practical theorizing, practitioners passed from an involved practical mode to a reflexive and quasi-theoretical one, and then, as exchanges proceeded, the other way around.

Study of a wind-wave numerical model and its integration with ocean and oil-spill numerical models

The ability to represent the transport and fate of an oil slick at the sea surface is a formidable task. By using an accurate numerical representation of oil evolution and movement in seawater, the possibility to asses and reduce the oil-spill pollution risk can be greatly improved. The blowing of the wind on the sea surface generates ocean waves, which give rise to transport of pollutants by wave-induced velocities that are known as Stokes’ Drift velocities. The Stokes’ Drift transport associated to a random gravity wave field is a function of the wave Energy Spectra that statistically fully describe it and that can be provided by a wave numerical model. Therefore, in order to perform an accurate numerical simulation of the oil motion in seawater, a coupling of the oil-spill model with a wave forecasting model is needed. In this Thesis work, the coupling of the MEDSLIK-II oil-spill numerical model with the SWAN wind-wave numerical model has been performed and tested. In order to improve the knowledge of the wind-wave model and its numerical performances, a preliminary sensitivity study to different SWAN model configuration has been carried out. The SWAN model results have been compared with the ISPRA directional buoys located at Venezia, Ancona and Monopoli and the best model settings have been detected. Then, high resolution currents provided by a relocatable model (SURF) have been used to force both the wave and the oil-spill models and its coupling with the SWAN model has been tested. The trajectories of four drifters have been simulated by using JONSWAP parametric spectra or SWAN directional-frequency energy output spectra and results have been compared with the real paths traveled by the drifters.

Membrane properties and synaptic integration of identified neuronal populations in the developing rodent neocortex

In my PhD work I concentrated on three elementary questions that are essential to understand the interactions between the different neuronal cell populations in the developing neocortex. The questions regarded the identity of Cajal-Retzius (CR) cells, the ubiquitous expression of glycine receptors in all major cell populations of the immature neocortex, and the role of taurine in the modulation of immature neocortical network activity.rnTo unravel whether CR cells of different ontogenetic origin have divergent functions I investigated the electrophysiological properties of YFP+ (derived from the septum and borders of the pallium) and YFP− CR cells (derived from other neocortical origins). This study demonstrated that the passive and active electrophysiological properties as well as features of GABAergic PSCs and glutamatergic currents are similar between both CR cell populations. These findings suggest that CR cells of different origins most probably support similar functions within the neuronal networks of the early postnatal cerebral cortex.rnTo elucidate whether glycine receptors are expressed in all major cell populations of the developing neocortex I analyzed the functional expression of glycine receptors on subplate (SP) cells. Activation of glycine receptors by glycine, -alanine and taurine elicited membrane responses that could be blocked by the selective glycinergic antagonist strychnine. Pharmacological experiments suggest that SP cells express functional heteromeric glycine receptors that do not contain 1 subunits. The activation of glycine receptors by glycine and taurine induced a membrane depolarization, which mediated excitatory effects. Considering the key role of SP cells in immature cortical networks and the development of thalamocortical connections, this glycinergic excitation may influence the properties of early cortical networks and the formation of cortical circuits.rnIn the third part of my project I demonstrated that tonic taurine application induced a massive increase in the frequency of PSCs. Based on their reversal potential and their pharmacological properties these taurine-induced PSCs are exclusively transmitted via GABAA receptors to the pyramidal neurons, while both GABAA and glycine receptors were implicated in the generation of the presynaptic activity. Accordingly, whole-cell and cell-attached recordings from genetically labeled interneurons revealed the expression of glycine and GABAA receptors, which mediated an excitatory action on these cells. These findings suggest that low taurine concentrations can tonically activate exclusively GABAergic networks. The activity level maintained by this GABAergic activity in the immature nervous system may contribute to network properties and can facilitate the activity dependent formation of adequate synaptic projections.rnIn summary, the results of my studies complemented the knowledge about neuronal interactions in the immature neocortex and improve our understanding of cellular processes that guide neuronal development and thus shape the brain.rn

Numerical assessment on the effective mechanical stimuli for matrix-associated metabolism in chondrocyte-seeded constructs

The self-regeneration capacity of articular cartilage is limited, due to its avascular and aneural nature. Loaded explants and cell cultures demonstrated that chondrocyte metabolism can be regulated via physiologic loading. However, the explicit ranges of mechanical stimuli that correspond to favourable metabolic response associated with extracellular matrix (ECM) synthesis are elusive. Unsystematic protocols lacking this knowledge produce inconsistent results. This study aims to determine the intrinsic ranges of physical stimuli that increase ECM synthesis and simultaneously inhibit nitric oxide (NO) production in chondrocyte-agarose constructs, by numerically re-evaluating the experiments performed by Tsuang et al. (2008). Twelve loading patterns were simulated with poro-elastic finite element models in ABAQUS. Pressure on solid matrix, von Mises stress, maximum principle stress and pore pressure were selected as intrinsic mechanical stimuli. Their development rates and magnitudes at the steady state of cyclic loading were calculated with MATLAB at the construct level. Concurrent increase in glycosaminoglycan and collagen was observed at 2300 Pa pressure and 40 Pa/s pressure rate. Between 0-1500 Pa and 0-40 Pa/s, NO production was consistently positive with respect to controls, whereas ECM synthesis was negative in the same range. A linear correlation was found between pressure rate and NO production (R = 0.77). Stress states identified in this study are generic and could be used to develop predictive algorithms for matrix production in agarose-chondrocyte constructs of arbitrary shape, size and agarose concentration. They could also be helpful to increase the efficacy of loading protocols for avascular tissue engineering. Copyright (c) 2010 John Wiley \& Sons, Ltd.

Monitoring and Assessment of Desertification and Land Degradation: Knowledge Management, Institutions and Economics: White Paper of the DSD Working Group 3

The White Paper is a review of leading scientific knowledge on the role of knowledge management, institutions and economics in monitoring and assessment of land degradation and desertification. It provides key recommendations for more effective policies and actions for combating desertification both withn the UNCCD and beyond. This White Paper is the result of an international collaboration and consultation led jointly by the Association of DesertNet International and the United Nations University - Institute for Water, Environment and Health (UNU-INWEH), of the Dryland Science for Development Consortium (DSD). The findings were presented at the First UNCCD Scientific Conference held during the COP-9 in Buenos Aires, 2009.

Knowledge Management and Decision Support for Sustainable Land Management

Much research has focused on desertification and land degradation assessments without putting sufficient emphasis on prevention and mitigation, although the concept of sustainable land management (SLM) is increasingly being acknowledged. A variety of SLM measures have already been applied at the local level, but they are rarely adequately recognised, evaluated, shared or used for decision support. WOCAT (World Overview of Technologies and Approaches) has developed an internationally recognised, standardised methodology to document and evaluate SLM technologies and approaches, including spatial distribution, allowing the sharing of SLM knowledge worldwide. The recent methodological integration into a participatory process allows now analysing and using this knowledge for decision support at the local and national level. The use of the WOCAT tools stimulates evaluation (self-evaluation as well as learning from comparing experiences) within SLM initiatives where all too often there is not only insufficient monitoring but also a lack of critical analysis. The comprehensive questionnaires and database system facilitate to document, evaluate and disseminate local experiences of SLM technologies and their implementation approaches. This evaluation process - in a team of experts and together with land users - greatly enhances understanding of the reasons behind successful (or failed) local practices. It has now been integrated into a new methodology for appraising and selecting SLM options. The methodology combines a local collective learning and decision approach with the use of the evaluated global best practices from WOCAT in a concise three step process: i) identifying land degradation and locally applied solutions in a stakeholder learning workshop; ii) assessing local solutions with the standardised WOCAT tool; iii) jointly selecting promising strategies for implementation with the help of a decision support tool. The methodology has been implemented in various countries and study sites around the world mainly within the FAO LADA (Land Degradation Assessment Project) and the EU-funded DESIRE project. Investments in SLM must be carefully assessed and planned on the basis of properly documented experiences and evaluated impacts and benefits: concerted efforts are needed and sufficient resources must be mobilised to tap the wealth of knowledge and learn from SLM successes.

Webinar Training: an acceptable, feasible and effective approach for multi-site medical record abstraction: the BOWII experience

Background Abstractor training is a key element in creating valid and reliable data collection procedures. The choice between in-person vs. remote or simultaneous vs. sequential abstractor training has considerable consequences for time and resource utilization. We conducted a web-based (webinar) abstractor training session to standardize training across six individual Cancer Research Network (CRN) sites for a study of breast cancer treatment effects in older women (BOWII). The goals of this manuscript are to describe the training session, its participants and participants' evaluation of webinar technology for abstraction training. Findings A webinar was held for all six sites with the primary purpose of simultaneously training staff and ensuring consistent abstraction across sites. The training session involved sequential review of over 600 data elements outlined in the coding manual in conjunction with the display of data entry fields in the study's electronic data collection system. Post-training evaluation was conducted via Survey Monkey©. Inter-rater reliability measures for abstractors within each site were conducted three months after the commencement of data collection. Ten of the 16 people who participated in the training completed the online survey. Almost all (90%) of the 10 trainees had previous medical record abstraction experience and nearly two-thirds reported over 10 years of experience. Half of the respondents had previously participated in a webinar, among which three had participated in a webinar for training purposes. All rated the knowledge and information delivered through the webinar as useful and reported it adequately prepared them for data collection. Moreover, all participants would recommend this platform for multi-site abstraction training. Consistent with participant-reported training effectiveness, results of data collection inter-rater agreement within sites ranged from 89 to 98%, with a weighted average of 95% agreement across sites. Conclusions Conducting training via web-based technology was an acceptable and effective approach to standardizing medical record review across multiple sites for this group of experienced abstractors. Given the substantial time and cost savings achieved with the webinar, coupled with participants' positive evaluation of the training session, researchers should consider this instructional method as part of training efforts to ensure high quality data collection in multi-site studies.

Distribution and Transmission of Medicinal Plant Knowledge in the Andean Highlands: A Case Study from Peru and Bolivia

This paper presents a study of patterns in the distribution and transmission of medicinal plant knowledge in rural Andean communities in Peru and Bolivia. Interviews and freelisting exercises were conducted with 18 households at each study site. The amount of medicinal plant knowledge of households was compared in relation to their socioeconomic characteristics. Cluster analysis was applied to identify households that possessed similar knowledge. The different modes of knowledge transmission were also assessed. Our study shows that while the amount of plant knowledge is determined by individual motivation and experience, the type of knowledge is influenced by the community of residence, age, migratory activity, and market integration. Plant knowledge was equally transmitted vertically and horizontally, which indicates that it is first acquired within the family but then undergoes transformations as a result of subsequent contacts with other knowledge sources, including age peers.

Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal single nucleotide polymorphism (SNP)-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LD-based actual effective population size was estimated in the range of 87-149, whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes, requiring knowledge of recent history (<50 generations), approximation assuming constant recombination rate seemed adequate.