scholarly journals “Here comes Bio-me”: An analysis of a biobank campaign targeted at children

2021 ◽  
pp. 096366252110226
Author(s):  
Karoliina Snell ◽  
Heta Tarkkala
Keyword(s):  
Seventeenth Century ◽  
Biological Material ◽  
Double Helix ◽  
Data Driven ◽  
Scientific Practices ◽  
Embryological Development ◽  
Age Appropriate

Finnish biobanks have started to recruit children. The national supervising authority has emphasized the centrality of providing children with age-appropriate information. We analyzed one such campaign. We argue that by simplifying the complex socio-technical arrangements of biobanking with the introduction of a new metaphor-like concept, “Bio-me,” the campaign presents a misleading and reductionist picture of data-driven biomedicine and biobank participation. First, the Bio-me character seems to bear similarities to the seventeenth-century explanations of embryological development. Second, the focus in the campaign is on biological material while crucial connections to different sorts of data are ignored. Third, we point to the absence of verbal references to genes and DNA, although the prevailing visualization comprises the double helix. We argue that the campaign has potential to contribute to public misunderstanding of science by introducing a new term that has little connection to actual biology or scientific practices it tries to promote.

Finding ‘anonymous’ in the digital archives: The problem of Arden of Faversham

2019 ◽  
Vol 34 (4) ◽  
pp. 855-873 ◽  
Author(s):  
Gary Taylor
Keyword(s):  
Seventeenth Century ◽  
Data Driven ◽  
Digital Archives ◽  
Dramatic Works ◽  
Commercial Theater ◽  
Arden Of Faversham

AbstractThis investigation re-examines debates about the authorship of the play Arden of Faversham, first published (anonymously) in 1592, and sometimes attributed to Shakespeare, Kyd, or Marlowe. More generally, it seeks to explain why modern data-driven attribution methods, which have created consensus about the authorship of The Revenger's Tragedy and other seventeenth-century plays, have failed to produce consistent results for plays written for the London commercial theaters in the years up to 1594. It proposes that attribution problems in that period can be better understood if plays are tested against authorial canons that include non-dramatic as well as dramatic works, using algorithms based on the evidence of n-grams and collocations, which seem not to be genre-dependent. It tests a sample passage from Scene 10 of Arden against the digital canons of fifteen writers known or suspected to have been writing for the commercial theater in the period 1585–92, using primarily EEBO-TCP. All tests identify the author as the poet, translator, and playwright Thomas Watson (1555–92). These data do not establish Watson's authorship of the entire play but open several new lines of enquiry for Arden and other anonymous and collaborative early plays.

Material Piety: Science and Religious Culture in Seventeenth-Century Portugal

2021 ◽  
Vol 74 (4) ◽  
pp. 1162-1209
Author(s):  
Nuno Castel-Branco
Keyword(s):  
Seventeenth Century ◽  
Early Modern ◽  
Early Modern Period ◽  
Science And Religion ◽  
Religious Culture ◽  
Scientific Practices ◽  
Modern Period ◽  
Religious Devotion

In seventeenth-century Lisbon, Jesuit mathematicians taught their students how to build blood-ejecting crucifixes and similar religious devices. Together with the activities of experts in the canonization of Isabel of Portugal and in other contexts, these situations represent rare instances in which religious devotion interacted directly with science. Informed by the histories of science, art, and religion, this essay argues that a piety centered on materiality fostered these scientific practices, which became religious ministries in themselves. This analysis brings new light to lasting debates on science and religion and to the purpose of practicing science in the early modern period.

Things and Data in Recent Biology

2018 ◽  
Vol 48 (5) ◽  
pp. 648-658
Author(s):  
Soraya de Chadarevian
Keyword(s):  
Life Cycle ◽  
Biological Material ◽  
Data Science ◽  
Data Driven ◽  
Special Issue ◽  
Data Link ◽  
Use Of Data ◽  
Data Practices ◽  
In Silico Biology ◽  
Biological World

There is much talk about data-driven and in silico biology, but how exactly does it work? This essay reflects on the relation of data practices to the biological things from which they are abstracted. Looking at concrete examples of computer use in biology, the essay asks: How are biological things turned into data? What organizes and limits the combination, querying, and re-use of data? And how does the work on data link back to the organismic or biological world? Considering the life cycle of data, the essay suggests that data remain linked to the biological material and the concrete context from which they are extracted and to which they always refer back. Consequently, the transition to data science is never complete. This essay is part of a special issue entitled Histories of Data and the Database edited by Soraya de Chadarevian and Theodore M. Porter.

scholarly journals Alcohol Use Disrupts Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach

2021 ◽  
Author(s):  
Delin Sun ◽  
Viraj R Adduru ◽  
Rachel D Phillips ◽  
Heather C Bouchard ◽  
Aristeidis Sotiras ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Cortical Thickness ◽  
Region Of Interest ◽  
Structural Mri ◽  
Data Driven ◽  
Age Cohorts ◽  
Cortical Thinning ◽  
Longitudinal Effects ◽  
Data Driven Approach ◽  
Age Appropriate

Objective: Cortical thickness changes dramatically during development and is influenced by adolescent drinking. However, previous findings have been inconsistent and limited by region-of-interest approaches that are underpowered because they do not conform to the underlying heterogeneity from the effects of alcohol. Methods: Adolescents (n=657; 12-22 years at baseline) from the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) who endorsed little to no alcohol use at baseline were assessed with structural MRI and followed longitudinally at four yearly intervals. Seven unique spatially covarying patterns of cortical thickness were obtained from the baseline scans by applying a novel data-driven method called non-negative matrix factorization (NMF). The cortical thickness maps of all participants' longitudinal scans were projected onto vertex-level cortical patterns to obtain participant-specific coefficients for each pattern. Linear mixed-effects models were fit to each pattern to investigate longitudinal effects of alcohol consumption on cortical thickness. Results: In most NMF-derived cortical thickness patterns, the longitudinal rate of decline in no/low drinkers was similar for all age cohorts, among moderate drinkers the decline was faster in the younger cohort and slower in the older cohort, among heavy drinkers the decline was fastest in the younger cohort and slowest in the older cohort (FDR corrected p-values < 0.01). Conclusions: The NMF method can delineate spatially coordinated patterns of cortical thickness at the vertex level that are unconstrained by anatomical features. Age-appropriate cortical thinning is more rapid in younger adolescent drinkers and slower in older adolescent drinkers.

scholarly journals ASigNTF: Agnostic Signature using NTF – a universal agnostic strategy to estimate cell-types abundance from transcriptomic datasets

2021 ◽  
Author(s):  
Paul Fogel ◽  
Galina Boldina ◽  
Corinne Rocher ◽  
Charles Bettembourg ◽  
George Luta ◽  
...  
Keyword(s):  
Biological Material ◽  
Ad Hoc ◽  
Immune Cell ◽  
Cell Types ◽  
Data Driven ◽  
Molecular Signatures ◽  
Tensor Factorization ◽  
Rna Seq ◽  
Data Driven Approach

AbstractBackgroundMolecular signatures for deconvolution of immune cell types have been proposed, based on a methodology that relies on the biological classification of the cell types being studied. When working with less known biological material, a data-driven approach is needed to uncover the underlying classes and construct ad hoc signatures.ResultsWe introduce a new approach, ASigNTF: Agnostic Signature using Non-negative Tensor Factorization, to perform the deconvolution of cell types from transcriptomics data (RNAseq and microarray). ASigNTF, which is based on two complementary statistical/mathematical tools: non-negative tensor factorization (for dimensionality reduction) and the Herfindahl-Hirschman index (for signature selection), can be applied to any type of tissue as long as transcriptomic data on isolated cells is available. As a direct result of the new method, we propose two new signatures for the deconvolution of immune cell types, one consisting of a relatively small set of 415 genes, which is more compatible with microarray platforms, and a larger set of 915 genes. Using external datasets, our two signatures outperform the CIBERSORT LM22 signature in deconvolution of RNA-seq data. Our signature with 415 genes allows to recognize a larger number of cell types compared to the ABIS microarray signature.ConclusionsThe paper proposes a new method, ASigNTF; applies the method, and also provides a software implementation that allows to identify molecular signatures for deconvolution of complex tissues and specifically up to 16 immune cell types from micro-array or RNA-seq data.HighlightsSeveral signatures of immune cell types have been proposed, which follow a methodology deeply rooted in the known biological classification of the investigated cell types.When working with less known biological material, a more agnostic, data-driven approach is required to uncover the underlying classes and construct ad hoc signatures.We present ASigNTF, a new agnostic approach to cell type classification and signature selection supported by an application software.We discuss the results of benchmarking our proposed signatures, ABIS-seq and CIBERSORT on external datasets.

scholarly journals Law for Computer Scientists and Other Folk

2020 ◽  
Author(s):  
Mireille Hildebrandt
Keyword(s):  
Rule Of Law ◽  
Legal Theory ◽  
Data Driven ◽  
Legal Rights ◽  
Scientific Practices ◽  
Legal Practice ◽  
Computing Systems ◽  
The Rule Of Law ◽  
Computer Scientists ◽  
Coherent Picture

This book introduces law to computer scientists. Computer scientists develop, protect, and maintain computing systems in the broad sense of that term, whether hardware, software, or data. They may be focused on e.g. digital security, or on embedded systems, or on software science. The aim of this book is to convey the internal logic of legal practice, firmly grounded in legal theory. It attempts to bridge the gap between two scientific practices, and probe the middle ground to present a reasonably coherent picture of the grammar and vocabulary of law and the rule of law. This attempt is geared toward those with no wish to become lawyers but who are nevertheless forced to consider the salience of legal rights and obligations. Simultaneously, this book aims to help lawyers to review their own trade. It is a volume on law in an onlife world, presenting a coherent picture of how modern law operates, how it emerged in the context of printed text, and how it confronts its new, data-driven environment.

Drinking Modulates Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach

2021 ◽  
Vol 89 (9) ◽  
pp. S274
Author(s):  
Delin Sun ◽  
Viraj Adduru ◽  
Rachel Phillips ◽  
Aristeidis Sotiras ◽  
Andrew Michael ◽  
...  
Keyword(s):  
Data Driven ◽  
Cortical Thinning ◽  
Data Driven Approach ◽  
Age Appropriate

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

A Simple Dichromatic Stain for Plastic Embedded Tissues

1970 ◽  
Vol 28 ◽  
pp. 296-297 ◽  
Author(s):  
G. R. Mackay ◽  
M. L. Mead
Keyword(s):  
Electron Microscopy ◽  
Toluidine Blue ◽  
Biological Material ◽  
Good Reproducibility ◽  
Routine Work ◽  
Staining Techniques

Color contrasting of 1 to 2 micron sections of plastic embedded biological material is an important adjunct to electron microscopy. The procedures in general use today are simple and rapid giving monochromatic results, e.g., toluidine blue. Although many di- and polychromatic histologic staining techniques have been modified to obtain a counterstaining effect with plasticembedded tissue, the methods are usually undesirable for routine work because they are time consuming, complicated and often defy good reproducibility.

Ultrathin frozen sections of yeast without aldehyde prefixation

1978 ◽  
Vol 36 (2) ◽  
pp. 58-59
Author(s):  
K. J. Böhm ◽  
a. E. Unger
Keyword(s):  
Aqueous Solutions ◽  
Biological Material ◽  
Yeast Cells ◽  
Frozen Sections ◽  
Good Preservation ◽  
Ultrathin Frozen Sections

During the last years it was shown that also by means of cryo-ultra-microtomy a good preservation of substructural details of biological material was possible. However the specimen generally was prefixed in these cases with aldehydes.Preparing ultrathin frozen sections of chemically non-prefixed material commonly was linked up to considerable technical and manual expense and the results were not always satisfying. Furthermore, it seems to be impossible to carry out cytochemical investigations by means of treating sections of unfixed biological material with aqueous solutions.We therefore tried to overcome these difficulties by preparing yeast cells (S. cerevisiae) in the following manner:

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