Until recently, retention of introns in mature mRNAs has been regarded as a consequence of mis‐splicing. Intron‐retaining transcripts are thought to be non‐functional because they are readily degraded by nonsense‐mediated decay. However, recent advances in next‐generation sequencing technologies have enabled the detection of numerous transcripts that retain introns. As we review herein, intron‐retaining mRNAs play an essential conserved role in normal physiology and an emergent role in diverse diseases. Intron retention should no longer be overlooked (...) as a key mechanism that independently reduces gene expression in normal biology. Exploring its contribution to the development and/or maintenance of diseases is of increasing importance. (shrink)

The explosion in sequencing technologies has provided us with an instrument to describe mammalian transcriptomes at unprecedented depths. This has revealed that alternative splicing is used extensively not only to generate protein diversity, but also as a means to regulate gene expression post‐transcriptionally. Intron retention (IR) is overwhelmingly perceived as an aberrant splicing event with little or no functional consequence. However, recent work has now shown that IR is used to regulate a specific differentiation event within the haematopoietic (...) system by coupling it to nonsense‐mediated mRNA decay (NMD). Here, we highlight how IR and, more broadly, alternative splicing coupled to NMD (AS‐NMD) can be used to regulate gene expression and how this is deregulated in disease. We suggest that the importance of AS‐NMD is not restricted to the haematopoietic system but that it plays a prominent role in other normal and aberrant biological settings. (shrink)

The expression of protein‐encoding genes is a complex process culminating in the production of mature mRNA and its translation by the ribosomes. The production of a mature mRNA involves an intricate series of processing steps. The majority of eukaryotic protein‐encoding genes contain intron sequences that disrupt the protein‐encoding frame, and hence have to be removed from immature mRNA prior to translation into protein. The mechanism involved in the selection of correct splice sites is incompletely understood. A considerable body of (...) evidence suggests that the splicing machinery has suboptimal efficiency and fidelity leading to substantial processing inaccuracy. Here we discuss a recently published article1 that extends observations that cells rely on nonsense‐mediated mRNA decay (NMD) to compensate for such suboptimal processing accuracy. Intriguingly these authors provide evidence for a strong selective pressure in favour of premature termination of mRNA translation in the event of intron retention. The analysis presented implies a positive role of NMD in transcript diversification through alternative splicing and suggest that this ancient surveillance mechanism may have co‐evolved with intron acquisition born from the need for quality control of splicing patterns. BioEssays 30:926–928, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Although introns in 5′‐ and 3′‐untranslated regions (UTRs) are found in many protein coding genes, rarely are they considered distinctive entities with specific functions. Indeed, mammalian transcripts with 3′‐UTR introns are often assumed nonfunctional because they are subject to elimination by nonsense‐mediated decay (NMD). Nonetheless, recent findings indicate that 5′‐ and 3′‐UTR intron status is of significant functional consequence for the regulation of mammalian genes. Therefore these features should be ignored no longer.

Knowing how introns originated should greatly enhance our understanding of the information we carry in our DNA. Gilbert’s suggestion that introns initially arose to facilitate recombination still stands, though not for the reason he gave. Reanney’s alternative, that evolution, from the early “RNA world” to today’s DNA-based world, would require the ability to detect and correct errors by recombination, now seems more likely. Consistent with this, introns are richer than exons in the potential to extrude the stem-loop structures needed for (...) the homology search that can lead to heteroduplex formation and the recognition of base mismatches. In nucleic acid sequences that were unable concomitantly to encode sufficient stem-loop potential, protein-encoding potential was constrained to arise as segments (exons) interrupted by segments rich in stem-loop potential (introns). Thus, sequences with properties that we now deem intronic are likely to have preceded the emergence of exons. (shrink)

A gene's “expression profile” denotes the number of transcripts present relative to all other transcripts. The overall rate of transcript production is determined by transcription and RNA processing rates. While the speed of elongating RNA polymerase II has been characterized for many different genes and organisms, gene‐architectural features – primarily the number and length of exons and introns – have recently emerged as important regulatory players. Several new studies indicate that rapidly cycling cells constrain gene‐architecture toward short genes with a (...) few introns, allowing efficient expression during short cell cycles. In contrast, longer genes with long introns exhibit delayed expression, which can serve as timing mechanisms for patterning processes. These findings indicate that cell cycle constraints drive the evolution of gene‐architecture and shape the transcriptome of a given cell type. Furthermore, a tendency for short genes to be evolutionarily young hints at links between cellular constraints and the evolution of animal ontogeny. (shrink)

Purpose The information society has developed rapidly since the end of the twentieth century. Many countries (including Australia) have been looking at ways to protect their citizens against the variety of risks associated with the continued evolution of the internet. The Australian Federal Government in 2013 proposed data retention as one possible method of protecting Australian society and aiding law enforcement agencies to investigate and prosecute cyber-crime. Design/methodology/approach The aim of this paper is to consider the issue of data (...) retention from a stakeholder’s perspective by analysing the public submissions garnered by the Australian Federal Government and identify the key issues and concerns that were raised by these stakeholders. The paper used a qualitative approach to undertake theme analysis. Findings The paper shows the concerns and wishes that different stakes holders have regarding data retention within Australia. Originality/value This is a unique study into implementation of data retention at a national level, in terms of the paper focussing on Australia. (shrink)

This article presents a frame of reference allowing school organization leaders to adopt an integrated and coherent set of policies and strategies likely to intervene in the phenomenon of retention of school principals. This framework urges to think about retention in a sustainable and lifelong professional development. It is based on a review of literature which proposes a set of levers covering different areas relating to human resources management such as strategic planning, professional integration, training, supervision, exchange and (...) mutual help networks and a two-way administrative and instructional digital information system. (shrink)

This paper investigates the claims made by both Freudian psychoanalysic thought and Husserlian phenomenology about the unconscious. First, it is shown how Husserl incorporates a complex notion of the unconscious in his analysis of passive synthesis. With his notion of an unintentional reservoir of past retentions, Husserl articulates an unconscious zone that must be activated from consciousness in order to come to life. Second, it is explained how Husserl still does not account for the Freudian unconscious. Freud's unconscious could be (...) called, in phenomenological terms, a repressed retentional zone that differs from both near and far retention. Finally, an analysis is offered for the significance of this psychoanalytic argument for phenomenology. Does phenomenology provide a complete account of the psychical life of the subject without the Freudian unconscious? Does phenomenology suggest, as is often done, that Freud's discovery of the unconscious is a fantastical invention? Or, does the Freudian unconscious represent a true stumbling block for phenomenology? (shrink)

In eukaryotes, RNA trans‐splicing is an important RNA‐processing form for the end‐to‐end ligation of primary transcripts that are derived from separately transcribed exons. So far, three different categories of RNA trans‐splicing have been found in organisms as diverse as algae to man. Here, we review one of these categories: the trans‐splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. Trans‐spliced exons can be predicted from DNA sequences derived from a large number of (...) sequenced organelle genomes. Further molecular genetic analysis of mutants has unravelled proteins, some of which being part of high‐molecular‐weight complexes that promote the splicing process. Based on data derived from the alga Chlamydomonas reinhardtii, a model is provided which defines the composition of an organelle spliceosome. This will have a general relevance for understanding the function of RNA‐processing machineries in eukaryotic organelles. (shrink)

This article proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called “extended present” as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the abstract notion (...) of “biological inertia”. (shrink)

The topic of offender DNA databases and the retention of offender's DNA samples are issues that continue to generate debate between privacy advocates and forensic DNA scientists. Considered previously by both the Federal DNA Advisory Board and the National Commission on the Future of DNA Evidence, recommendations were made that the existing statutory frameworks were sufficient to protect the confidentiality and use of the DNA samples solely for forensic identification purposes and that the issue be revisited. Now, approximately five (...) years since these debates, privacy advocates and forensic scientists retain divergent views on this issue. This brief essay is not intended to fuel the debate, but rather, to describe the protections and safeguards currently in place for the protection of the offender DNA samples.Surrounding the discussion of the sample retention issue are the underlying principles for the establishment of the Combined DNA Index System Program and the National DNA Index System. (shrink)

The individual informed consent model remains critical to the ethical conduct and regulation of research involving human beings. Parental informed consent process in a rural setting of northern Ghana was studied to describe comprehension and retention among parents as part of the evaluation of the existing informed consent process.

Turning away from entities and focusing instead exclusively on ‘structural’ aspects of scientific theories has been advocated as a cogent response to objections levelled at realist conceptions of the aim and success of science. Physical theories whose (predictive) past successes are genuine would, in particular, share with their successors structural traits that would ultimately latch on to ‘structural’ features of the natural world. Motives for subscribing to Structural Realism are reviewed and discussed. It is argued that structural retention claims (...) lose their force if one gives up merely historical readings of the transition from Galilean-relativistic classical mechanics to the ‘special’ theory of relativity, heeding instead basic requirements that lead to their common derivation. Further cause for scepticism is found upon realising that the basic mathematical framework of quantum theory essentially reflects its predictive purpose, without any necessary input, be it of a ‘structural’ kind, from the physical world. (shrink)

Concerning cases involving temporal indexicals Kaplan has argued that Fregean thoughts cannot be the bearers of cognitive significance due to the alleged fact that one can think the same thought from one occasion to the next without realizing this—thus linking the issue of cognitive significance to that of belief retention. Kaplan comes up with his own version of the Fregean strategy for accounting for belief retention that does not face this kind of a problem; but he finds it (...) deficient because it leads us to implausibly deny that one who is lost in time retains the beliefs one held before this occurred. I take issue with Kaplan though in conformity with his plausible demands about belief retention and argue that a situation does not arise in which one can fail to realize that one is thinking the same thought from one occasion to the next. I also argue that thoughts are the bearers of cognitive significance as well as explanatory of belief retention. (shrink)

High temporal resolution event-related brain potential and electroencephalographic coherence studies of the neural substrate of short-term storage in working memory indicate that the sustained coactivation of both prefrontal cortex and the posterior cortical systems that participate in the initial perception and comprehension of the retained information are involved in its storage. These studies further show that short-term storage mechanisms involve an increase in neural synchrony between prefrontal cortex and posterior cortex and the enhanced activation of long-term memory representations of material (...) held in short-term memory. This activation begins during the encoding/comprehension phase and evidently is prolonged into the retention phase by attentional drive from prefrontal cortex control systems. A parsimonious interpretation of these findings is that the long-term memory systems associated with the posterior cortical processors provide the necessary representational basis for working memory, with the property of short-term memory decay being primarily due to the posterior system. In this view, there is no reason to posit specialized neural systems whose functions are limited to those of short-term storage buffers. Prefrontal cortex provides the attentional pointer system for maintaining activation in the appropriate posterior processing systems. Short-term memory capacity and phenomena such as displacement of information in short-term memory are determined by limitations on the number of pointers that can be sustained by the prefrontal control systems. Key Words: coherence; event-related potentials; imaging; long-term memory; memory; short-term memory; working memory. (shrink)

Taking organisational responses to the ?organ retention scandals? in the United Kingdom and Australia as a starting point, this paper considers the role of social welfare workers within the medico-legal system. Official responses to the inquiries of the late 1990s have focused on issues of consent and process-transparency, leaving unaddressed concerns expressed by the bereaved about the impact of organ retention on both their experience of grief and on the deceased themselves. A review of grief and embodiment literature (...) suggests that such concerns are consistent with the significance of relationship, attachment and identity within grief resolution?however that last problematic term is defined. The case example of an Australian coronial jurisdiction which has attempted to deal with some of these issues through mandating the discussion of autopsy and organ retention processes by grief counsellors with bereaved families is then provided. A distinction is drawn between these discussions and the seeking of consent. The discussion concludes by considering the ambiguous nature of the social welfare role within this contested field, suggesting that this ambiguity, while perhaps a source of flexibility in practice, may itself relate to a lack of clear information about the needs of the bereaved. This paper contributes to the development of that knowledge and offers some necessarily tentative recommendations regarding social welfare practice in this challenging arena. (shrink)

Previous research on cross-situational word learning has demonstrated that learners are able to reduce ambiguity in mapping words to referents by tracking co-occurrence probabilities across learning events. In the current experiments, we examined whether learners are able to retain mappings over time. The results revealed that learners are able to retain mappings for up to 1 week later. However, there were interactions between the amount of retention and the different learning conditions. Interestingly, the strongest retention was associated with (...) a learning condition that engendered retrieval dynamics that initially challenged the learner but eventually led to more successful retrieval toward the end of learning. The ease/difficulty of retrieval is a critical process underlying cross-situational word learning and is a powerful example of how learning dynamics affect long-term learning outcomes. (shrink)

A popular version of anti-Humeanism is one that views fundamental properties as being irreducibly dispositional in nature, and it is a view to which I am attracted. Proponents of this view typically object to Humean regularity theories of laws on the basis that they do not explain why our world is regular rather than chaotic from moment to moment. It is thought that, for this reason, Humeanism does not provide firm enough foundations for induction. However, in this paper I argue (...) that it is far from clear how these anti-Humeans can themselves explain this regularity. This is because it is far from clear how they can explain why the entities in our world do not change their dispositional properties arbitrarily over time. This is a neglected problem, which I call the retention problem. In an attempt to solve this problem, several naturalistic explanations of retention are explored. Unfortunately, none of these explanations is free of problems, showing that dispositional forms of anti-Humeanism may not have as many advantages as some have assumed where the problem of induction is concerned. (shrink)

Propositions are generally thought to have a truth-value only relative to some parameter or sequence of parameters. Many apparently straightforward notions, like what it is to disagree or retain a belief, become harder to explain once propositional truth is thus relativized. An account of disagreement within a framework involving such ‘stoic’ propositions is here presented. Some resources developed in that account are then used to respond to the eternalist charge that temporalist propositions can't function as belief contents because they don't (...) allow us to make adequate sense of what belief retention amounts to. (shrink)

In this paper I shall try to clarify Husserl’s conception of time-consciousness. In particular, I try to explain what exactly the asymmetry between protention and retention consists in. I argue (i) that Rodemeyer’s understanding of the protention-retention relationship, as developed, seems misleading, mainly for two reasons: first, it does not take into account that the ‘now’ has duration; second, she conceives the relation between protention and retention as symmetric, (ii) that the asymmetry between protention and retention (...) could be better understood if we could not only take into account the influence that retention and affect have on protention, but also if we could take into consideration the conceptual difference between surprise and disappointment. This difference, I suggest, reveals new ways to understand the protention-retention asymmetry. (shrink)

This paper explores difficulties around consent in the context of organ retention and return. It addresses the proposals of the Independent Review Group in Scotland on the Retention of Organs at Post Mortem to speak of authorisation rather than consent. Practical problems about whose consent determines disputes in relation to organ retention are explored. If a young child dies and his mother refuses consent but his father agrees what should ensue? Should the expressed wishes of a deceased (...) adult override the objections of surviving relatives? The paper suggests much broader understanding of the issues embedded in organ retention is needed to provide solutions which truly meet families' and society's needs. (shrink)

Retention of offender DNA samples serves an important quality assurance role for forensic DNA laboratories. Consistent with the principles of confidentiality underlying the establishment of the state and national DNA databases, safeguards are in place to protect the DNA samples from unauthorized use.

Since the mid-1990s most EU Member States have established a national forensic DNA database. These mass repositories of DNA profiles enable the police to identify DNA stains which are found at crime scenes and are invaluable in criminal investigation. Governments have always brushed aside privacy objections by stressing that the stored DNA profiles do not contain sensitive genetic information on the included individuals and that they reside under the statutory privacy protection regulations. However, it has been generally overlooked that the (...) police also store the DNA samples from which the DNA profiles are derived. Although these DNA samples are actually a potential source of genetic information, they have so far scarcely been the subject of discussion. In this article we will show that both European and national regulations offer inadequate protection to completely prevent function creep, that is, the use of these forensic DNA samples for purposes beyond those envisaged at the time of collection. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Retention, Reliability, and DedicationRenee J. TillmanI love what I do. I am a Hospice and Palliative Nurse Assistant. I have been for 16 years. I have worked in this field for 37 years—in long term care, private duty and home health. I still like getting up and going to work. I have a great work ethic. I think it came about when I started working for Leader Nursing (...) and Rehabilitation Center. My plans were to become a nurse, just like my mother. This employer believes that if he contributed to his employees by way of educating them he would accomplish two things. Loyal employees and highly skilled nurse aides. He knew we were the backbone of his center and believed in his strategy to give the very best care his employee's could provide.I was one of the first nursing assistants in the building. I started on the 11-7 shift, myself and a licensed vocational nurse (LVN). She was a gem. In a four story building. They had security for us. They started from the top and filled the building up. I was never so proud to be a nurse aide. Pretty soon we were filled. I worked the night shift for three years and decided to go to the day shift, 7 to 3. [End Page 154]It was then that I decided this profession was for me, and I was going to be the best. Everything we did was a learning experience. We received report at the beginning of our shift. We were asked to be on the job 15 minutes before shift, and we did so without pay. We felt it was important to get information to care for the residents. The incentives were what they called the Leader Ladder. This Ladder was there for you to climb to the highest occupation in the nursing field you wanted to go, with the help from the scholarship program in place. The goals of the employer were retention, reliability, support, and dedication from the employees.That is not in place today, especially in the long-term care settings. There is a revolving door in most places. In most places employees don't even have nametags. If they do have them, they're in the pockets just to swipe the clock. Uniforms are not decent, I mean wrinkle-free and clean. Even hair and faces are not groomed. Yes I see this today. We are the forgotten, the invisible. Shame on those watch dogs. When I was with Leader, I would watch my nurse do everything—catheters, suctioning, wound care—everything. We used to do wound care and finger sticks. In some places, they don't even let the aides do vital signs.One of the cases I will never forget, this was at a rehabilitation center with a floor that was skilled. This lady was admitted. She was only 60. She had the biggest tumor I had ever seen on the side of her neck; it was cancerous. The tumor was growing outside her neck. I was just 25. When we received report that morning, we were told of physical and history, where she was with her disease, and that she had come there to die. She had no family. We quickly became her family. She was tall and skinny with dark hair. We were also told how she would die and to be prepared so it would not be scary for her or for us. She was going to bleed to death from the tumor. But, our biggest challenge, you see, was not to show that there was an odor when in her room or where ever she was. The cancer was very foul-smelling. I think that is why she loved us; we acted like there was no smell. The day she died, her tumor started a steady flow of blood. She knew it was the end. We had dark towels for her, she lay in her bed, she was never left alone. We had our work to do, but she was never left alone. What I remember the most is her eyes; you see, she could not speak that day. She... (shrink)

A widely accepted view in the discussion of personal identity is that the notion of psychological continuity expresses a one--many or many--one relation. This belief is unfounded. A notion of psychological continuity expresses a one--many or many--one relation only if it includes, as a constituent, psychological properties whose relation with their bearers is one--many or many--one; but the relation between an indexical psychological state and its bearer when first tokened is not a one--many or many--one relation. It follows that not (...) all types of psychological continuity may take a one--many or many--one form. This conclusion casts doubt on the Lockean approach to the issue, by showing that the notion of psychological continuity Lockeans rely on may not be available. (shrink)