The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

The Anthropocene literature has brought attention to the plasticity and porosity of Earth systems under the dramatic impact of human activities. Moving across scales of analysis, this paper focuses attention on anthropogenic effects at the micro-scale of genomic regulation, neuronal functioning and cellular activity. Building on expanding dialogues at the interface of Anthropocene science, biogeography, microbiology and ecotoxicology, we mobilize epigenetic findings to show increasing evidence of anthropogenic changes in plants, animals and human bodies. Treating human-induced changes at the macro-global and micro-biological scales as part of an intertwined process has implications for how these problems are conceptualised and addressed. While we are sceptics about major geo-bio-social syntheses, we believe that agile social-scientific tools can facilitate interaction across disciplines without denying unevenness, and differences. If rightly contextualized in broad anthropological and social science frameworks, biosocial work on epigenetics offers a compelling avenue to make detectable the ‘slow violence’ of everyday pollution, racism, inequalities and the disproportionate impact of the Anthropocene on the poor and vulnerable. Consolidating work at the Anthropocene/biology interface has potential to offer a richer and more complete picture of the present crisis at the macro and micro-scale alike.

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A Wolf in Another Wolf’s Clothing: Post-Genomic Regulation Dictates Venom Profiles of Medically-Important Cryptic Kraits in India

Toxins ◽

10.3390/toxins13010069 ◽

2021 ◽

Vol 13 (1) ◽

pp. 69 ◽

Cited By ~ 1

Author(s):

Kartik Sunagar ◽

Suyog Khochare ◽

R. R. Senji Laxme ◽

Saurabh Attarde ◽

Paulomi Dam ◽

...

Keyword(s):

Negative Impact ◽

Indian Subcontinent ◽

Clinical Effectiveness ◽

Venom Gland ◽

Western India ◽

The Common ◽

Genomic Regulation

The Common Krait (Bungarus caeruleus) shares a distribution range with many other ‘phenotypically-similar’ kraits across the Indian subcontinent. Despite several reports of fatal envenomings by other Bungarus species, commercial Indian antivenoms are only manufactured against B. caeruleus. It is, therefore, imperative to understand the distribution of genetically distinct lineages of kraits, the compositional differences in their venoms, and the consequent impact of venom variation on the (pre)clinical effectiveness of antivenom therapy. To address this knowledge gap, we conducted phylogenetic and comparative venomics investigations of kraits in Southern and Western India. Phylogenetic reconstructions using mitochondrial markers revealed a new species of krait, Romulus’ krait (Bungarus romulusi sp. nov.), in Southern India. Additionally, we found that kraits with 17 mid-body dorsal scale rows in Western India do not represent a subspecies of the Sind Krait (B. sindanus walli) as previously believed, but are genetically very similar to B. sindanus in Pakistan. Furthermore, venom proteomics and comparative transcriptomics revealed completely contrasting venom profiles. While the venom gland transcriptomes of all three species were highly similar, venom proteomes and toxicity profiles differed significantly, suggesting the prominent role of post-genomic regulatory mechanisms in shaping the venoms of these cryptic kraits. In vitro venom recognition and in vivo neutralisation experiments revealed a strong negative impact of venom variability on the preclinical performance of commercial antivenoms. While the venom of B. caeruleus was neutralised as per the manufacturer’s claim, performance against the venoms of B. sindanus and B. romulusi was poor, highlighting the need for regionally-effective antivenoms in India.

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Genomic regulation of type 2 diabetes endophenotypes: Contribution from genetic studies in the Goto-Kakizaki rat

Biochimie ◽

10.1016/j.biochi.2017.08.012 ◽

2017 ◽

Vol 143 ◽

pp. 56-65 ◽

Cited By ~ 6

Author(s):

Marie-Thérèse Bihoreau ◽

Marc-Emmanuel Dumas ◽

Mark Lathrop ◽

Dominique Gauguier

Keyword(s):

Type 2 Diabetes ◽

Genetic Studies ◽

Genomic Regulation

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Critical genomic regulation mediated by Enhancer of Polycomb

Current Genetics ◽

10.1007/s00294-017-0742-3 ◽

2017 ◽

Vol 64 (1) ◽

pp. 147-154 ◽

Cited By ~ 7

Author(s):

Naomi E. Searle ◽

Lorraine Pillus

Keyword(s):

Genomic Regulation

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Airway Mucosal Host Defense Is Key to Genomic Regulation of Cystic Fibrosis Lung Disease Severity

American Journal of Respiratory and Critical Care Medicine ◽

10.1164/rccm.201701-0134oc ◽

2018 ◽

Vol 197 (1) ◽

pp. 79-93 ◽

Cited By ~ 25

Author(s):

Deepika Polineni ◽

Hong Dang ◽

Paul J. Gallins ◽

Lisa C. Jones ◽

Rhonda G. Pace ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Disease ◽

Disease Severity ◽

Host Defense ◽

Cystic Fibrosis Lung ◽

Cystic Fibrosis Lung Disease ◽

Genomic Regulation ◽

Lung Disease Severity

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Digital Play

Transforming K-12 Classrooms with Digital Technology - Advances in Early Childhood and K-12 Education ◽

10.4018/978-1-4666-4538-7.ch010 ◽

2014 ◽

pp. 193-207

Author(s):

Jennifer Howell ◽

Susan McDonald

Keyword(s):

Good Practice ◽

Digital Technologies ◽

Student Learning Outcomes ◽

Early Years ◽

Pedagogical Practices ◽

Formal Schooling ◽

Framework Technology ◽

Effective Use ◽

Early Childhood Settings ◽

New Framework

This chapter showcases a new framework (Technology and Play Framework) for teachers to consider when planning the use of digital technologies in the Early Years of formal schooling. It also presents the findings from a pilot study conducted with an F-1 (Foundation year and year 1) class in an Australian primary school that demonstrated how this framework could direct the effective use of a specific digital technology in terms of student learning outcomes with particular focus on literacy and numeracy. While play is recognised as an essential component of good practice in early childhood settings, it needs to be reconsidered and aligned to incorporate emerging digital technologies and complementary pedagogical practices in order to support authentic learning.

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Identity and Externalities toward Sustainability

Cases on SMEs and Open Innovation ◽

10.4018/978-1-61350-314-0.ch006 ◽

2012 ◽

pp. 100-125 ◽

Cited By ~ 1

Author(s):

Paola Francesca Spadaro ◽

Gianvito D’Aprile ◽

Maria Beatrice Ligorio ◽

Neil Schwartz

Keyword(s):

Discourse Analysis ◽

Focus Group ◽

Sense Of Community ◽

Sense Of Belonging ◽

Focus Group Discussions ◽

Group Discussions ◽

Negotiation Of Identity ◽

Framework Technology ◽

Definition Of

Two focus group discussions involving 14 entrepreneurs and 106 questionnaires administered to employees were analyzed to explore various parameters of externalities, such as: (1) how externality is conceived; (2) the interplay between a sense of community and a re-definition and negotiation of identity; (3) the role of technology; the sense of belonging, and (4) the propensity to collaborate. Data are analyzed through both thematic discourse analysis and quantitative frequencies analysis. Results show that entrepreneurs hold a multidimensional definition of externality, meditated by their professional and private experience. Ultimately, the reflection on externalities sustains a sense of innovation connected to multi-membership and to re-negotiation of the sense of identity. Within this framework, technology is conceived as a tool supporting the appropriation and sharing of externalities.

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Execution framework technology

Big Data in Astronomy ◽

10.1016/b978-0-12-819084-5.00004-3 ◽

2020 ◽

pp. 215-244

Author(s):

Ying Mei ◽

Rodrigo Tobar ◽

Chen Wu ◽

Hui Deng ◽

Shoulin Wei ◽

...

Keyword(s):

Framework Technology

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Experiments in Environment Integration

Principles of CASE Tool Integration ◽

10.1093/oso/9780195094787.003.0014 ◽

1994 ◽

Author(s):

Alan W. Brown ◽

David J. Carney ◽

Edwin J. Morris ◽

Dennis B. Smith ◽

Paul F. Zarrella

Keyword(s):

Production Quality ◽

Current Level ◽

Third Party ◽

Tool Integration ◽

Current State ◽

Internal Structures ◽

Framework Technology ◽

Per Se ◽

Development Approach ◽

Selection Of

In assembling a CASE environment from a collection of commercial off-theshelf (COTS) tools, tool users must find ways to connect the tools such that they provide adequate support for their particular software development approach. This task takes place in the context of limited knowledge of the tools, limited access to the source or internal structures of the tools, limited resources with which to perform and maintain the tool connections, and evolving understanding of the needs of the tool users. This places severe restrictions on what can be attempted in terms of tool interconnection. Environment framework technologies (e.g., ECMA PCTE, ATIS, BMS, ToolTalk, or CORBA) claim to provide a set of common integration services that aid in the tool integration process. There have been numerous discussions about the value, maturity, and complexity of these framework technologies. Such discussions are characterized by three points: general agreement that framework technology per se is a valuable goal to pursue; moderate disagreement as to whether the current level of framework technology is a sufficient basis for production quality CASE environments; and considerable disagreement about which of the current technologies are the most likely to mature and succeed. Notable about these discussions, however, is that there has not been extensive use of the technologies in question. This stems from several sources: their expense, their unfamiliarity and complexity to current tool users, and a widespread concern about their immaturity. This lack of use is perhaps understandable, but it has had the additional effect that partisans of one or another technology have made assertions based on little factual information about the relative merits of the technology in question. To expand our own expertise in tool integration and framework technologies, and to answer the question, “What tool integrations are possible for third-party tool users given the current state of COTS tools and integration technology?” we performed a set of experiments involving the integration of a collection of common COTS tools with environment framework technologies in support of a typical development scenario. Our selection of these tools and technologies was based on common availability and application to the development scenario(s) of interest.

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