scholarly journals Open Data for Open Questions in Comparative Nutrition

Insects ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 236 ◽  
Author(s):  
Juliano Morimoto ◽  
Mathieu Lihoreau
Keyword(s):  
Human Health ◽  
Nutrient Intake ◽  
Open Data ◽  
Nutritional Ecology ◽  
Comparative Framework ◽  
Open Questions ◽  
Nutrition Research ◽  
Wide Range ◽  
Animal Performances

Achieving a better understanding of the consequences of nutrition to animal fitness and human health is a major challenge of our century. Nutritional ecology studies increasingly use nutritional landscapes to map the complex interacting effects of nutrient intake on animal performances, in a wide range of species and ecological contexts. Here, we argue that opening access to these hard-to-obtain, yet considerably insightful, data is fundamental to develop a comparative framework for nutrition research and offer new quantitative means to address open questions about the ecology and evolution of nutritional processes.

scholarly journals Applicability of Honey on Silkworms (Bombyx mori) and Quality Improvement of Its Biomaterials

2021 ◽  
Vol 11 (10) ◽  
pp. 4613
Author(s):  
Gabriela-Maria Baci ◽  
Alexandra-Antonia Cucu ◽  
Adela Ramona Moise ◽  
Daniel Severus Dezmirean
Keyword(s):  
Quality Improvement ◽  
Bombyx Mori ◽  
Human Health ◽  
Recombinant Proteins ◽  
Therapeutic Agent ◽  
Life Sciences ◽  
Model Organism ◽  
Medical Field ◽  
Wide Range ◽  
Ancient Times

Since ancient times, honey has been considered one of the most illustrious and esteemed natural products. Honey plays two key roles; specifically, it is an appreciated nutritional product, and also exhibits a wide range of beneficial properties for human health as a therapeutic agent. Furthermore, it has been shown that honey has valuable effects on the biological and physiological features of mulberry silkworms (Bombyx mori). Bombyx mori exhibits importance not only for the economy, but it also serves as an important biotechnological bioreactor for the production of recombinant proteins that have a great impact in the medical field and beyond. It also represents an important model organism for life sciences. In view of the fact that silk fibroin serves as a natural biopolymer that displays high biocompatibility with human organisms and due to honey’s various and remarkable properties for human health, the two elements are currently used together in order to develop ideal biomaterials for a wide range of purposes. In this review, by discussing the applicability of honey on Bombyx mori and beyond, the importance of honey for life sciences and related fields is spotlighted.

scholarly journals Ways into Understanding HIF Inhibition

Cancers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 159
Author(s):  
Tina Schönberger ◽  
Joachim Fandrey ◽  
Katrin Prost-Fingerle
Keyword(s):  
Protein Interactions ◽  
Target Genes ◽  
Protein Protein Interactions ◽  
Low Oxygen ◽  
Drug Candidates ◽  
Open Questions ◽  
Wide Range ◽  
Hif Pathway

Hypoxia is a key characteristic of tumor tissue. Cancer cells adapt to low oxygen by activating hypoxia-inducible factors (HIFs), ensuring their survival and continued growth despite this hostile environment. Therefore, the inhibition of HIFs and their target genes is a promising and emerging field of cancer research. Several drug candidates target protein–protein interactions or transcription mechanisms of the HIF pathway in order to interfere with activation of this pathway, which is deregulated in a wide range of solid and liquid cancers. Although some inhibitors are already in clinical trials, open questions remain with respect to their modes of action. New imaging technologies using luminescent and fluorescent methods or nanobodies to complement widely used approaches such as chromatin immunoprecipitation may help to answer some of these questions. In this review, we aim to summarize current inhibitor classes targeting the HIF pathway and to provide an overview of in vitro and in vivo techniques that could improve the understanding of inhibitor mechanisms. Unravelling the distinct principles regarding how inhibitors work is an indispensable step for efficient clinical applications and safety of anticancer compounds.

scholarly journals Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 275
Author(s):  
Natsuko Matsumoto ◽  
Jonguk Park ◽  
Rie Tomizawa ◽  
Hitoshi Kawashima ◽  
Koji Hosomi ◽  
...  
Keyword(s):  
Individual Differences ◽  
Environmental Factors ◽  
Gut Microbiota ◽  
Human Health ◽  
Negative Correlation ◽  
Nutrient Intake ◽  
Monozygotic Twins ◽  
Human Gut ◽  
Positive Correlation ◽  
Human Gut Microbiota

Background and Objectives: The gut microbiota is associated with human health and dietary nutrition. Various studies have been reported in this regard, but it is difficult to clearly analyze human gut microbiota as individual differences are significant. The causes of these individual differences in intestinal microflora are genetic and/or environmental. In this study, we focused on differences between identical twins in Japan to clarify the effects of nutrients consumed on the entire gut microbiome, while excluding genetic differences. Materials and Methods: We selected healthy Japanese monozygotic twins for the study and confirmed their zygosity by matching 15 short tandem repeat loci. Their fecal samples were subjected to 16S rRNA sequencing and bioinformatics analyses to identify and compare the fluctuations in intestinal bacteria. Results: We identified 12 genera sensitive to environmental factors, and found that Lactobacillus was relatively unaffected by environmental factors. Moreover, we identified protein, fat, and some nutrient intake that can affect 12 genera, which have been identified to be more sensitive to environmental factors. Among the 12 genera, Bacteroides had a positive correlation with retinol equivalent intake (rs = 0.38), Lachnospira had a significantly negative correlation with protein, sodium, iron, vitamin D, vitamin B6, and vitamin B12 intake (rs = −0.38, −0.41, −0.39, −0.63, −0.42, −0.49, respectively), Lachnospiraceae ND3007 group had a positive correlation with fat intake (rs = 0.39), and Lachnospiraceae UCG-008 group had a negative correlation with the saturated fatty acid intake (rs = −0.45). Conclusions: Our study is the first to focus on the relationship between human gut microbiota and nutrient intake using samples from Japanese twins to exclude the effects of genetic factors. These findings will broaden our understanding of the more intuitive relationship between nutrient intake and the gut microbiota and can be a useful basis for finding useful biomarkers that contribute to human health.

Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments

2003 ◽  
Vol 01 (03) ◽  
pp. 541-586 ◽  
Author(s):  
Tero Aittokallio ◽  
Markus Kurki ◽  
Olli Nevalainen ◽  
Tuomas Nikula ◽  
Anne West ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Analysis ◽  
Microarray Data ◽  
Microarray Data Analysis ◽  
Biological Research ◽  
Microarray Experiments ◽  
Dna Microarray Data ◽  
Open Questions ◽  
Analysis Technique ◽  
Wide Range

Microarray analysis has become a widely used method for generating gene expression data on a genomic scale. Microarrays have been enthusiastically applied in many fields of biological research, even though several open questions remain about the analysis of such data. A wide range of approaches are available for computational analysis, but no general consensus exists as to standard for microarray data analysis protocol. Consequently, the choice of data analysis technique is a crucial element depending both on the data and on the goals of the experiment. Therefore, basic understanding of bioinformatics is required for optimal experimental design and meaningful interpretation of the results. This review summarizes some of the common themes in DNA microarray data analysis, including data normalization and detection of differential expression. Algorithms are demonstrated by analyzing cDNA microarray data from an experiment monitoring gene expression in T helper cells. Several computational biology strategies, along with their relative merits, are overviewed and potential areas for additional research discussed. The goal of the review is to provide a computational framework for applying and evaluating such bioinformatics strategies. Solid knowledge of microarray informatics contributes to the implementation of more efficient computational protocols for the given data obtained through microarray experiments.

scholarly journals Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 534 ◽  
Author(s):  
Cristian Pasquaretta ◽  
Tamara Gómez-Moracho ◽  
Philipp Heeb ◽  
Mathieu Lihoreau
Keyword(s):  
Social Behavior ◽  
Gut Microbiota ◽  
Social Interactions ◽  
Nutritional Ecology ◽  
Social Consequences ◽  
Complex Interactions ◽  
Wide Range ◽  
Nutritional Geometry ◽  
Social Animals

Microbes influence a wide range of host social behaviors and vice versa. So far, however, the mechanisms underpinning these complex interactions remain poorly understood. In social animals, where individuals share microbes and interact around foods, the gut microbiota may have considerable consequences on host social interactions by acting upon the nutritional behavior of individual animals. Here we illustrate how conceptual advances in nutritional ecology can help the study of these processes and allow the formulation of new empirically testable predictions. First, we review key evidence showing that gut microbes influence the nutrition of individual animals, through modifications of their nutritional state and feeding decisions. Next, we describe how these microbial influences and their social consequences can be studied by modelling populations of hosts and their gut microbiota into a single conceptual framework derived from nutritional geometry. Our approach raises new perspectives for the study of holobiont nutrition and will facilitate theoretical and experimental research on the role of the gut microbiota in the mechanisms and evolution of social behavior.

Self-reports of health-care utilization: Diary or questionnaire?

2005 ◽  
Vol 21 (3) ◽  
pp. 298-304 ◽  
Author(s):  
Mandy van den Brink ◽  
Wilbert B. van den Hout ◽  
Anne M. Stiggelbout ◽  
Hein Putter ◽  
Cornelis J. H. van de Velde ◽  
...  
Keyword(s):  
Health Care ◽  
Health Care Utilization ◽  
Convergent Validity ◽  
Cost Utility ◽  
Care Utilization ◽  
Economic Evaluations ◽  
Cost Diary ◽  
Open Questions ◽  
Wide Range ◽  
More Care

Objectives:The feasibility and convergent validity of a cost diary and a cost questionnaire was investigated.Methods:Data were obtained as part of a cost-utility analysis alongside a multicenter clinical trial in patients with resectable rectal cancer. A sample of 107 patients from 30 hospitals was asked to keep a weekly diary during the first 3 months after surgery, and a monthly diary from 3 to 12 months after surgery. A second sample of seventy-two patients from twenty-eight hospitals in the trial received a questionnaire at 3, 6, and 12 months after surgery, referring to the previous 3 or 6 months. Format and items of the questions were similar and included a wide range of medical and nonmedical items and costs after hospitalization for surgery.Results:Small differences were found with respect to nonresponse (range, 79 to 86 percent) and missing questions (range, 1 to 6 percent between the diary and questionnaire). For most estimates of volumes of care and of costs, the diary and questionnaire did not differ significantly. Total 3-month nonhospital costs were €1,860, €1,280, and €1,050 in the diary sample and €1,860, €1,090, and €840 in the questionnaire sample at 3, 6, and 12 months after surgery, respectively (p=.50). However, with respect to open questions, the diary sample tended to report significantly more care.Conclusions:For the assessment of health-care utilization in economic evaluations alongside clinical trials, a cost questionnaire with structured closed questions may replace a cost diary for recall periods up to 6 months.

scholarly journals Cross-border Investigations on the Prevalence and Transmission Dynamics of Cryptosporidium Species in Dairy Cattle Farms in Western Mainland Europe

2021 ◽  
Author(s):  
Pedro Pinto ◽  
Claudia A Ribeiro ◽  
Sumaiya Hoque ◽  
Ourida Hammouma ◽  
Hélène Leruste ◽  
...  
Keyword(s):  
The Netherlands ◽  
Human Health ◽  
Dna Sequences ◽  
Significant Risk ◽  
Dairy Farms ◽  
Economic Loss ◽  
Cryptosporidium Spp ◽  
Wide Range ◽  
Parasitic Protist ◽  
Cattle Farms

Cryptosporidium is comprised an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis. In cattle farms, the incidence of cryptosporidiosis results in high mortality in calves leading to considerable economic loss in the livestock industry. Infected animals may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in calves. This poses a significant risk to other farms via breeding centres, to trading of livestock and to human health. This study, funded by the Interreg-2-seas programme, is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, 1084 faecal samples, corresponding to 57 dairy-farms from all three countries, were analysed. Well-established protocols amplifying the 18S rDNA and gp60 genes fragments, followed by DNA sequencing, were used for the detection and subtyping C. parvum; the DNA sequences obtained were further characterised using a combination of bioinformatics and phylogenetics methods. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also detected in humans. Consequently, this study highlights how widespread is C. parvum in dairy farms and endorses cattle as a major carrier of zoonotic C. parvum subtypes, which subsequently pose a significant threat to human health.

scholarly journals NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

2020 ◽  
Vol 6 ◽  
Author(s):  
Christoph Steinbeck ◽  
Oliver Koepler ◽  
Felix Bach ◽  
Sonja Herres-Pawlis ◽  
Nicole Jung ◽  
...  
Keyword(s):  
Data Management ◽  
Data Science ◽  
Open Data ◽  
Research Data ◽  
Data Standards ◽  
Data Repositories ◽  
Data Infrastructure ◽  
Research Data Management ◽  
Wide Range ◽  
Chemistry Community

The vision of NFDI4Chem is the digitalisation of all key steps in chemical research to support scientists in their efforts to collect, store, process, analyse, disclose and re-use research data. Measures to promote Open Science and Research Data Management (RDM) in agreement with the FAIR data principles are fundamental aims of NFDI4Chem to serve the chemistry community with a holistic concept for access to research data. To this end, the overarching objective is the development and maintenance of a national research data infrastructure for the research domain of chemistry in Germany, and to enable innovative and easy to use services and novel scientific approaches based on re-use of research data. NFDI4Chem intends to represent all disciplines of chemistry in academia. We aim to collaborate closely with thematically related consortia. In the initial phase, NFDI4Chem focuses on data related to molecules and reactions including data for their experimental and theoretical characterisation. This overarching goal is achieved by working towards a number of key objectives: Key Objective 1: Establish a virtual environment of federated repositories for storing, disclosing, searching and re-using research data across distributed data sources. Connect existing data repositories and, based on a requirements analysis, establish domain-specific research data repositories for the national research community, and link them to international repositories. Key Objective 2: Initiate international community processes to establish minimum information (MI) standards for data and machine-readable metadata as well as open data standards in key areas of chemistry. Identify and recommend open data standards in key areas of chemistry, in order to support the FAIR principles for research data. Finally, develop standards, if there is a lack. Key Objective 3: Foster cultural and digital change towards Smart Laboratory Environments by promoting the use of digital tools in all stages of research and promote subsequent Research Data Management (RDM) at all levels of academia, beginning in undergraduate studies curricula. Key Objective 4: Engage with the chemistry community in Germany through a wide range of measures to create awareness for and foster the adoption of FAIR data management. Initiate processes to integrate RDM and data science into curricula. Offer a wide range of training opportunities for researchers. Key Objective 5: Explore synergies with other consortia and promote cross-cutting development within the NFDI. Key Objective 6: Provide a legally reliable framework of policies and guidelines for FAIR and open RDM.

Characterising RDF data sets

2017 ◽  
Vol 44 (2) ◽  
pp. 203-229 ◽  
Author(s):  
Javier D Fernández ◽  
Miguel A Martínez-Prieto ◽  
Pablo de la Fuente Redondo ◽  
Claudio Gutiérrez
Keyword(s):  
Data Structures ◽  
Large Scale ◽  
Open Data ◽  
Structural Features ◽  
Data Sets ◽  
Data Set ◽  
Wide Range ◽  
Rdf Data ◽  
Description Framework ◽  
Resource Description

The publication of semantic web data, commonly represented in Resource Description Framework (RDF), has experienced outstanding growth over the last few years. Data from all fields of knowledge are shared publicly and interconnected in active initiatives such as Linked Open Data. However, despite the increasing availability of applications managing large-scale RDF information such as RDF stores and reasoning tools, little attention has been given to the structural features emerging in real-world RDF data. Our work addresses this issue by proposing specific metrics to characterise RDF data. We specifically focus on revealing the redundancy of each data set, as well as common structural patterns. We evaluate the proposed metrics on several data sets, which cover a wide range of designs and models. Our findings provide a basis for more efficient RDF data structures, indexes and compressors.

Armchair Auditors: Crowdsourcing Analysis of Government Expenditures

2015 ◽  
Vol 12 (1) ◽  
pp. 71-91 ◽  
Author(s):  
Daniel E. O'Leary
Keyword(s):  
United Kingdom ◽  
Local Governments ◽  
Open Data ◽  
Information And Communications Technology ◽  
Government Expenditures ◽  
Data Movement ◽  
The United Kingdom ◽  
Wide Range ◽  
Potential Benefits ◽  
Open Data Movement

ABSTRACT Increasingly, there is interest in using information and communications technology (ICT) to help build a “better world.” As an example, the United Kingdom has initiated an “open data” movement to disclose financial information about federal and local governments and other organizations. This has led to the use of a wide range of technologies (Internet, Databases, Web 2.0, etc.) to facilitate disclosure. However, since there is a huge cost of generating and maintaining open data, there also is a concern: “will anyone do anything with the data?” In a speech in 2009, David Cameron, the Prime Minister of the United Kingdom, used the term “armchair auditor” to describe crowdsourcing analysis of that data. In that speech, Cameron (2009) noted: “Just imagine the effect that an army of armchair auditors is going to have on those expense claims.” Accordingly, as more and more countries and organizations generate open data, those “armchair auditors” could play an increasingly important role: to help crowdsource monitoring of government expenditures. This paper investigates a number of potential benefits and a number of emerging concerns associated with armchair auditors.

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