Prediction and Topological Models in Neuroscience

In the last two decades, philosophy of neuroscience has predominantly focused on explanation. Indeed, it has been argued that mechanistic models are the standards of explanatory success in neuroscience over, among other things, topological models. However, explanatory power is only one virtue of a scientific model. Another is its predictive power. Unfortunately, the notion of prediction has received comparatively little attention in the philosophy of neuroscience, in part because predictions seem disconnected from interventions. In contrast, we argue that topological predictions can and do guide interventions in science, both inside and outside of neuroscience. Topological models allow researchers to predict many phenomena, including diseases, treatment outcomes, aging, and cognition, among others. Moreover, we argue that these predictions also offer strategies for useful interventions. Topology-based predictions play this role regardless of whether they do or can receive a mechanistic interpretation. We conclude by making a case for philosophers to focus on prediction in neuroscience in addition to explanation alone

Network analysis for food safety: Quantitative and structural study of data gathered through the RASFF system in the European Union.

This paper reports a quantitative and structural analysis of data gathered on the food issues reported by the European Union members over the last forty years. The study applies statistical measures and network analysis techniques. For this purpose, a graph was constructed of how different contaminated products have been distributed through countries. The work aims to leverage insights into the structure formed by the involvement of European countries in the exchange of goods that can cause problems for populations. The results obtained show the roles of different countries in the detection of sensitive routes. In particular, the analysis identifies problematic origin countries, such as China or Turkey, whereas European countries, in general, do have good border control policies for the import/export of food.pre-print1210 K

Apis Mellifera Animal Study in a Role Perspective Using the Bibliometrix Tools (SLNA Method Application)

There is no research on the study of Apis mellifera using bibliometrix tools. This study aims to determine the results of the study of Apis mellifera in a role perspective using Bibliometrix Tools. This study uses an approach that uses the Systematic Literature Network Analysis (SLNA) method assisted by bibliometrix tools in the form of four applications OpenRefine, VOSviewer, Bibliometrix, and Tableau Public. The data source used is the Scopus database. This study uses a confirmability test. Journals that publish many articles about Apis mellifera include Apidologie, Insects, and Scientific Reports. Authors who publish a lot of articles about Apis mellifera include Neumann P number 32, Chen Y and Le Conte Y number 20. The years that published a lot of articles about Apis mellifera are 2021 and 2020. The theme network consists of 5 clusters the farther the distance between topics it means that people rarely research about the topic/theme. Apis mellifera is the dominant pollinating insect that helps in the process of pollinating many plants such as blueberries and other roles, namely as medicine, from propolis to honey bee cocoons. Meanwhile, the detrimental role caused by Apis mellifera honey bees and other pollinating insects is as a vector of diseases that causes the carrying of bad bacteria that can attack plants which of course will reduce production yields

Hydrology, limnology and environmental feasibility of the Pareja Limno-reservoir

Sastre Merlín, Antonio, codir.Los grandes embalses en áreas de clima mediterráneo generan una serie de impactos ambientales y económicos negativos. Una actuación innovadora para mitigarlos es la construcción de pequeños diques en sectores de cola de dichos embalses, que dan lugar a la aparición de una masa de agua diseñada para mantener un nivel constante y para la que hemos propuesto el término "limnoembalse". El Limnoembalse de Pareja, primero diseñado con una doble finalidad ambiental y recreativa, fue construido en 2006 junto al pueblo homónimo y es alimentado por el río Ompólveda. Se ubica en el área del embalse de Entrepeñas (provincia de Guadalajara), afectado por los citados impactos. A pesar del interés de esta infraestructura, parece oportuno adquirir conocimiento sobre su comportamiento. Esta tesis doctoral tiene como objetivo caracterizar la cuenca del río Ompólveda y el Limnoembalse de Pareja, evaluando su viabilidad ambiental. La aportación del río Ompólveda supone un 10% de la precipitación media, con un 60-70% de flujo de base que mantiene un caudal permanente en ausencia de lluvias. Sin embargo, el mantenimiento de un nivel de agua constante en el limnoembalse no queda garantizado durante el estiaje en años secos. Además, la simulación de escenarios de cambio climático con el modelo SWAT apunta a una disminución de la aportación de hasta un 50%, lo que supondría un descenso notable del nivel del agua y cuestiona la viabilidad hidrológica de la infraestructura. Por otra parte, el estudio hidrogeoquímico de la cuenca reveló que la disolución de calcita y yeso son los procesos dominantes, evolucionaldo la composición del agua de bicarbonatada cálcica a sulfatada cálcica y aumentando su conductividad. El Limnoembalse de Pareja sigue una dinámica de lago monomíctico templado, con un agua ligeramente alcalina y de alta conductividad. Las comunidades de fitoplancton, zooplancton y microorganismos están dominadas por diatomeas, rotíferos y oligotrofos, respectivamente. La calidad del agua resulta adecuada para los usos previstos del limnoembalse. Diversos indicadores sugirieron un estatus oligo-mestorófico y un estado ecológico Muy Bueno. Las concentraciones de microorganismos fecales fueron acordes con la legislación. No obstante, la calidad puede empeorar en invierno (mayor transporte de nutrientes y microorganismos) y en verano (mayor conductividad y proliferación de algas). Además, las simulaciones de cambio climático predicen un deterioro futuro del estado trófico. También se ha estudiado el régimen de erosión de la cuenca del río Ompólveda y el aterramiento del limnoembalse mediante una metodología in-situ, sencilla y económica. La erosión bruta media en la cuenca se estima en 6 T ha-1 año -1. No obstante, la tasa anual de aterramiento en el Limnoembalse de Pareja fue aproximadamente un 0,29%. Ello supone que supone que sólo un 3,9% de los sedimentos movilizados en la cuenca alcanzan el limnoembalse -posiblemente debido a la baja conectividad-, lo que garantizaría la viabilidad ambiental del Limnoembalse de Pareja desde el punto de vista del riesgo de aterramiento. Los resultados obtenidos en esta tesis doctoral podrían tener relevancia en el ámbito de la gestión del agua, puesto que aportan conocimiento y metodologías para la evaluación multidisciplinar de estas nuevas masas de agua

Hydrology, limnology and environmental feasibility of the Pareja Limno-reservoir

Sastre Merlín, Antonio, codir.Los grandes embalses en áreas de clima mediterráneo generan una serie de impactos ambientales y económicos negativos. Una actuación innovadora para mitigarlos es la construcción de pequeños diques en sectores de cola de dichos embalses, que dan lugar a la aparición de una masa de agua diseñada para mantener un nivel constante y para la que hemos propuesto el término "limnoembalse". El Limnoembalse de Pareja, primero diseñado con una doble finalidad ambiental y recreativa, fue construido en 2006 junto al pueblo homónimo y es alimentado por el río Ompólveda. Se ubica en el área del embalse de Entrepeñas (provincia de Guadalajara), afectado por los citados impactos. A pesar del interés de esta infraestructura, parece oportuno adquirir conocimiento sobre su comportamiento. Esta tesis doctoral tiene como objetivo caracterizar la cuenca del río Ompólveda y el Limnoembalse de Pareja, evaluando su viabilidad ambiental. La aportación del río Ompólveda supone un 10% de la precipitación media, con un 60-70% de flujo de base que mantiene un caudal permanente en ausencia de lluvias. Sin embargo, el mantenimiento de un nivel de agua constante en el limnoembalse no queda garantizado durante el estiaje en años secos. Además, la simulación de escenarios de cambio climático con el modelo SWAT apunta a una disminución de la aportación de hasta un 50%, lo que supondría un descenso notable del nivel del agua y cuestiona la viabilidad hidrológica de la infraestructura. Por otra parte, el estudio hidrogeoquímico de la cuenca reveló que la disolución de calcita y yeso son los procesos dominantes, evolucionaldo la composición del agua de bicarbonatada cálcica a sulfatada cálcica y aumentando su conductividad. El Limnoembalse de Pareja sigue una dinámica de lago monomíctico templado, con un agua ligeramente alcalina y de alta conductividad. Las comunidades de fitoplancton, zooplancton y microorganismos están dominadas por diatomeas, rotíferos y oligotrofos, respectivamente. La calidad del agua resulta adecuada para los usos previstos del limnoembalse. Diversos indicadores sugirieron un estatus oligo-mestorófico y un estado ecológico Muy Bueno. Las concentraciones de microorganismos fecales fueron acordes con la legislación. No obstante, la calidad puede empeorar en invierno (mayor transporte de nutrientes y microorganismos) y en verano (mayor conductividad y proliferación de algas). Además, las simulaciones de cambio climático predicen un deterioro futuro del estado trófico. También se ha estudiado el régimen de erosión de la cuenca del río Ompólveda y el aterramiento del limnoembalse mediante una metodología in-situ, sencilla y económica. La erosión bruta media en la cuenca se estima en 6 T ha-1 año -1. No obstante, la tasa anual de aterramiento en el Limnoembalse de Pareja fue aproximadamente un 0,29%. Ello supone que supone que sólo un 3,9% de los sedimentos movilizados en la cuenca alcanzan el limnoembalse -posiblemente debido a la baja conectividad-, lo que garantizaría la viabilidad ambiental del Limnoembalse de Pareja desde el punto de vista del riesgo de aterramiento. Los resultados obtenidos en esta tesis doctoral podrían tener relevancia en el ámbito de la gestión del agua, puesto que aportan conocimiento y metodologías para la evaluación multidisciplinar de estas nuevas masas de agua

Comparative evaluation of cheese whey microbial composition from four Italian cheese factories by viable counts and 16S rRNA gene amplicon sequencing

The microbiota of cheese whey from four dairy companies located in the North-East of Italy was evaluated during winter and spring using both culture-dependent and culture-independent methods. Although no significant differences were observed (p > 0.05) for any of the six microbial categories analysed by plate counting among the dairy companies, significant differences at the family and genus level were revealed by linear discriminant analysis (LDA). In particular, variations in the abundance of the families Pseudomonadaceae and Enterobacteriaceae, as well as of the genus Acinetobacter were observed and positively correlated with plate count results (p < 0.05). The combined use of culture-dependent and culture-independent approaches gave a better description of the hygienic conditions and food safety aspects and could therefore be suggested as a useful integrated approach. \ua9 2020 Elsevier Lt

Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.

Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities

A New Approach to Analyzing Patterns of Collaboration in Co-authorship Networks - Mesoscopic Analysis and Interpretation

This paper focuses on methods to study patterns of collaboration in co-authorship networks at the mesoscopic level. We combine qualitative methods (participant interviews) with quantitative methods (network analysis) and demonstrate the application and value of our approach in a case study comparing three research fields in chemistry. A mesoscopic level of analysis means that in addition to the basic analytic unit of the individual researcher as node in a co-author network, we base our analysis on the observed modular structure of co-author networks. We interpret the clustering of authors into groups as bibliometric footprints of the basic collective units of knowledge production in a research specialty. We find two types of coauthor-linking patterns between author clusters that we interpret as representing two different forms of cooperative behavior, transfer-type connections due to career migrations or one-off services rendered, and stronger, dedicated inter-group collaboration. Hence the generic coauthor network of a research specialty can be understood as the overlay of two distinct types of cooperative networks between groups of authors publishing in a research specialty. We show how our analytic approach exposes field specific differences in the social organization of research.Comment: An earlier version of the paper was presented at ISSI 2009, 14-17 July, Rio de Janeiro, Brazil. Revised version accepted on 2 April 2010 for publication in Scientometrics. Removed part on node-role connectivity profile analysis after finding error in calculation and deciding to postpone analysis

Developing a ‘best practice’ supply chain performance and operational framework for dairy producers : a multiple case study analysis in Egypt

Supply chain management is based on the global concept, where different companies are connected worldwide. Moreover, supply chain performance management is a growing field of study, especially for perishable products. Egyptian dairy producers have suffered a significant drop in their production since 2011, due to the poor quality and quantity of raw milk, changes in governmental regulations, hazard risks, and volatility in consumer taste. This has threatened meeting the increasing market demand for dairy products. Extant literature highlighted the following gaps: limited research assessing the dairy producers' supply chain performance in a detailed view from an operational perspective, and lack of specific performance measures especially in Egypt as a developing country in this context. Therefore, this thesis introduces a best practice performance framework for dairy producers in Egypt to optimise and assess their performance, in terms of sustainable production of safe and secure dairy products to fulfil the Egyptian market demand. The research adopts three theories to explore and understand the research problem. The resource-based view theory is used to identify the operational capabilities and the critical control points within the production. Network theory is used to explore the risks in the wider dairy supply chain and identify solutions to overcome them. Last, the institutional theory is used to understand the pressures faced by dairy producers, all of which will help to develop a best practice performance framework by following the mimetic approach to contrast and compile the performance measures of the top six large Egyptian dairy producers. That is achieved by referring to the Supply Chain Operation Reference (SCOR) model key attributes as a guide. This research utilises a narrative literature review to consolidate the background knowledge on the dairy sector’s operations and supply chain risks. Then, classify the different operational and supply chain performance measures and models to provide future research directions based on the research gaps identified. A multiple case-study methodology is adopted in this study. It follows a qualitative research approach across two phases by using the NVivo12 software to conduct a thematic analysis. Firstly, two observations and seventeen exploratory semi structured interviews with key informants within six case studies were conducted to explore the operational capabilities, critical control points and performance measures and the risks affecting large Egyptian dairy producers. Secondly, two focus groups were held with a diversified sample of practitioners, government officials, and suppliers to validate the results of the first phase. The key findings of the research highlighted that those dairy producers performing on a satisfactory level qualify them to adopt the SCOR model to enhance their performance and imitate the dairy producers’ practices in developed countries. The following key areas were addressed: 1) identifying the current operational capabilities needed to produce milk products, defining and classifying new critical control points for the production of UHT milk and pasteurised milk which up until now remains vague and not well determined, 2) each producer has designed their performance measures which has left them exposed to vulnerabilities and limits their optimum utilisation of their capabilities and to be able to continually improve. Thus, standardisation of performance measures and sharing of best practice, with a detailed classification for applicability is key for Egyptian dairy producers. A major contribution of this research is the development of an operational and supply chain performance-based best practice framework, based on SCOR, to guide the dairy producers through optimising and enhancing their production of safe and secure dairy products. Further, the research has identified three new SCOR attributes: a) suppliers’ improvement and traceability, b) health and safety environment, and c) employees’ morale, also seven new critical control points and capabilities. Besides, utilising the qualitative approach to provide in-depth within and cross-case exploration of six large dairy producers’ current state. This research also recommends that the government should leverage the small farmers within a milk hub, with a tracking system, to close the gap of raw milk supply shortage to Egypt. That addresses the shortcomings in the extant literature, which will significantly contribute to enhancing the performance and sustainability of the Egyptian dairy industry as a whole, and consequently will benefit the Egyptian economy. That sets the base for future researchers to utilise the proposed best practice for a wider scope of dairy producers with similar characteristics

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.T32GM008764 - NIGMS NIH HHS; T32 GM008764 - NIGMS NIH HHS; R01 DE024468 - NIDCR NIH HHS; R01 GM121950 - NIGMS NIH HHS; DE-SC0012627 - Biological and Environmental Research; RGP0020/2016 - Human Frontier Science Program; NSFOCE-BSF 1635070 - National Science Foundation; HR0011-15-C-0091 - Defense Advanced Research Projects Agency; R37DE016937 - NIDCR NIH HHS; R37 DE016937 - NIDCR NIH HHS; R01GM121950 - NIGMS NIH HHS; R01DE024468 - NIDCR NIH HHS; 1457695 - National Science FoundationPublished versio