Quantitative Biology

Many studies have shown that the geographic origin is one of the most influencing factors in the choice of olive oil. To avoid misleading, European regulation has established specific rules to report the geographical origin of extra virgin and virgin olive oils on the product label, but an official analytical procedure to verify this information has not been yet defined. In this work, a flash gas chromatography untargeted approach for determination of volatile compounds, followed by a chemometric data elaboration, is proposed for discrimination of EVOOs and VOOs according to their geographical origin (EU and Extra-EU). A set of 210 samples was analyzed and two different classification techniques were used, one linear and one non-linear. The two models were also validated using an external data set. Satisfactory results were obtained for both chemometric approaches: considering the PLS-DA, 89% and 81% of EU and Extra-EU samples, respectively, were correctly classified; for ANN the percentages were 93% and 89%, respectively. These results confirm the reliability of the method as a rapid approach to discriminate EVOOs and VOOs according to their geographical provenance.

In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered researchers and practitioners at the crossing point between information technology and agricultural science, to study all aspects in the life cycle of semantic resources: conceptualization, edition, sharing, standardization, services, alignment, long term support. First, the working group realized a landscape study, a study of the uses of semantics in agrifood, then collected use cases for the exploitation of semantics resources-a generic term to encompass vocabularies, terminologies, thesauri, ontologies. The resulting requirements were synthesized into 39 "hints" for users and developers of semantic resources, and providers of semantic resource services. We believe adopting these recommendations will engage agrifood sciences in a necessary transition to leverage data production, sharing and reuse and the adoption of the FAIR data principles. The paper includes examples of adoption of those requirements, and a discussion of their contribution to the field of data science.

Tumor-induced angiogenesis is the formation of new sprouts from preexisting nearby parent blood vessels. Computationally, tumor-induced angiogenesis can be modeled using cellular automata (CA), partial differential equations, etc. In this present study, a realistic physiological approach has been made to model the process of angiogenesis by using 3D CA model. CA technique uses various neighborhoods like Von-Neumann neighborhood, Moore neighborhood, and Margolus neighborhood. In our model Von-Neumann neighborhood has used for distribution of some significant chemical and non-chemical tumor angiogenic factors like vascular endothelial growth factor, endothelial cells, O2, extracellular matrix, fibronectin, etc., and Moore neighborhood is used for distribution of matrix metalloproteinase. In vivo tumor environment all the factors are not distributed equally in the extracellular matrix. Distributions of those chemical and nonchemical factors depend on their source, nature and function. To keep similarity with the biological tumor environment, we have formulated initial distributions of the chemical and non-chemical factors accordingly. We have started the simulation in MATLAB with this initial distribution. Number of sprouts randomly varies from one run to another. We observed that sprouts are not originating from the same locations in each simulation. A sprout has high sensitivity of VEGF and fibronectin concentrations. sVEGFR-1 always tries to regress the sprout. When two or more sprouts come closer, they merge with each other leading to anastomosis. Sufficient number of tip cells may cause sprout towards tumor.

Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general mathematical construct to model the wide spectrum of context-dependence, eludes the students of biology. An objective and rigorous model, from both 'bottom-up' as well as 'top-down' perspective, is proposed here to serve as the template to describe the various kinds of context-dependence that we encounter in different branches of biology. Interactions between biological contexts was found to be transitive but non-commutative. It is found that a hierarchical nature of dependence amongst the biological contexts models the emergent biological properties efficiently. Reasons for these findings are provided with a general model to describe biological reality. Scheme to algorithmically implement the hierarchic structure of organization of biological contexts was achieved with a construct named 'Context tree'. A 'Context tree' based analysis of context interactions among biophysical factors influencing protein structure was performed.

This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal ...) and properly biological (heart beating, respiration, metabolic ...). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the usual (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The "visual" representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3-dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for "representation time", with a cognitive significance.

Reproductive phenology, growth and mortality rates are key ecological parameters that determine population dynamics and are therefore of vital importance to stock assessment models for fisheries management. In many fish species, the spawning phenology is sensitive to environmental factors that modulate or trigger the spawning event, which differ between regions and seasons. In addition, climate change may also alter patterns of reproductive phenology at the community level. Usually, hatch-date distributions are determined back-calculating the age estimated on calcified structures from the capture date. However, these estimated distributions could be biased due to mortality processes or time spaced samplings derived from fishery. Here, we present a Bayesian approach that functions as a predictive model for the hatching date of individuals from a fishery-dependent sampling with temporal biases. We show that the shape and shift of the observed distribution is corrected. This model can be applied in fisheries with multiple cohorts, for species with a wide geographical distribution and living under contrasting environmental regimes and individuals with different life histories such as thermo-dependent growth, length-dependent mortality rates, etc.

The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures of biological systems remains unsettled. Here, we present a broader perspective on biological organization and how quantum-like dynamics and coherence might shape the very fabric from which complex biological systems are organized. Regardless of its exact nature, a unique form of coherence seems apparent at multiple scales in biology and its better characterization may have broad consequences for the understanding of living organisms as complex systems.

As of 2020, COVID-19 is spreading in the world. In Japan, the Ministry of Health, Labor and Welfare developed COVID-19 Contact-Confirming Application (COCOA). The researches to examine the effect of COCOA are still not sufficient. We develop a mathematical model to examine the effect of COCOA and show examined result.

Chimeric antigen receptor T cells (CAR T cells) are dosed similarly to donor lymphocyte infusions following hematopoietic cell transplantation. In this perspective paper a mathematical basis for personalized dosing of CAR T cells is introduced.

Biological and biomedical imaging datasets record the constitution, architecture and dynamics of living organisms across several orders of magnitude of space and time. Imaging technologies are now used throughout the life and biomedical sciences to achieve discovery and understanding of biological mechanisms in the basic sciences as well as assessment, diagnosis and therapeutic intervention in clinical trials and animal and human medicine. The universal application and use of imaging raises an important question and opportunity: what is the value and ultimate destination of biological and medical imaging data? In the last few years, several informatics and data science technologies have matured sufficiently so that routine publication of these datasets is now possible. Participants in Global BioImaging from 15 countries and all populated continents have agreed on the need for recommendations and guidelines for the establishment of image data repositories and the formats they use for delivering data to the global scientific community. This white paper presents a shared, global view of criteria for these common, globally applicable guidelines and provisional proposals for open tools and resources that are available now and can provide a foundation for future development.