The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations

Complete mitochondrial genomes have proven extremely valuable in helping to understand the evolutionary relationships among metazoans. However, uneven taxon sampling may lead to unclear or even erroneous phylogenetic topologies. The decapod crustaceans are relatively well-sampled, but sampling is still uneven within this group. We have sequenced the mitochondrial genomes of two shrimps Litopenaeus vannamei and Fenneropenaeus chinensis. As seen in other metazoans, the genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. The gene arrangements are consistent with the pancrustacean ground pattern. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial protein-coding genes strengthened the support that Caridea and Palinura are primitive members of Pleocyemata. These sequences, in combination with two previously published penaeid mitochondrial genomes, suggest that genera within the family Penaeidae have the following relationship: (((Penaeits + Fenneropenaett.) + Litopeiiaelts) + Marsupenaeus). The analyses of nucleic acid and amino acid sequences of the mitochondrial genomes also strongly support the monophyly of Penaeidae, Brachyura and Pleocyemata. In addition, the analyses of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group.

Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA (His) gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

Deconstructing 'Mono'-Lingualism: considerations of value for 'English' 'language' education in a global setting.

Traditionally, language speakers are categorised as mono-lingual, bilingual, or multilingual. It is traditionally assumed in English language education that the ‘lingual’ is something that can be ‘fixed’ in form, written down to be learnt, and taught. Accordingly, the ‘mono’-lingual will have a ‘fixed’ linguistic form. Such a ‘form’ differs according to a number of criteria or influences including region or ‘type’ of English (for example, World Englishes) but is nevertheless assumed to be a ‘form’. ‘Mono-lingualism’ is defined and believed, traditionally, to be ‘speaking one language’; wherever that language is; or whatever that language may be. In this chapter, grounded in an individual subjective philosophy of language, we question this traditional definition. Viewing language from the philosophical perspectives such as those of Bakhtin and Voloshinov, we argue that the prominence of ‘context’ and ‘consciousness’ in language means that to ‘fix’ the form of a language goes against the very spirit of how it is formed and used. We thus challenge the categorisation of ‘mono’-lingualism; proposing that such a categorisation is actually a category error, or a case ‘in which a property is ascribed to a thing that could not possibly have that property’ (Restivo, 2013, p. 175), in this case the property of ‘mono’. Using this proposition as a starting point, we suggest that more time be devoted to language in its context and as per its genuine use as a vehicle for consciousness. We theorise this can be done through a ‘literacy’ based approach which fronts the context of language use rather than the language itself. We outline how we envision this working for teachers, students and materials developers of English Language Education materials in a global setting. To do this we consider Scotland’s Curriculum for Excellence as an exemplar to promote conscious language use in context.

The Where, Who, When and Why of Medieval Welsh Prose Texts: Some Methodological Considerations

Rodway, S. (2007). The Where, Who, When and Why of Medieval Welsh Prose Texts: Some Methodological Considerations. Studia Celtica. 41, pp.47-89. RAE2008

Characteristics of preferred gait patterns: considerations for exercise prescription

Gait patterns have been widely studied in different fields of science for their particular characteristics. A dynamic approach of human locomotion considers walking and running as two stable behaviors adopted spontaneously under certain levels and natures of constraints. When no constraints are imposed, people naturally prefer to walk at the typical speed (i.e., around 4.5 km.h-1) that minimizes metabolic energy cost. The preferred walking speed (PWS) is also known to be an indicator of mobility and an important clinical factor in tracking impairements in motor behaviors. When constrained to move at higher speeds (e.g., being late), people naturally switch their preference to running for similar optimization reasons (e.g., physiological, biomechanical, perceptual, attentionnal costs). Indeed, the preferred transition speed (PTS) marks the natural seperation between walking and running and consistently falls within a speed range around 7.5 km.h-1. This chapter describes the constraint-dependant spontaneous organisation of the locomotor system, specifically on the walk-to-run speed continuum. We provide examples of the possibility of long-term adaptations of preferred behaviors to specific constraints such as factors related to traditional clothing or practice. We use knowledge from studies on preferred behaviors and on the relationship between affect and exercise adherence as a backdrop to prescribing a walk exercise program with an emphasis on populations with overweight or obesity.

The Deve­lop­ment of Leibniz’s Con­si­de­ra­tions in John Yench’s Pro­ject

The purpose of the article is to present John Yench’s a priori language as a continuation of Leibniz’s idea. Before I proceed to show the project of the Inter-Disciplinary International Reference Language, I would like to discuss the development of Gottfried Wilhelm Leibniz’s view on artificial languages. I will try to show the evolution of Leibniz’s universal language: from its ideal conception to a tool which formalizes the whole of human knowledge. Also, I will show Leibniz’s influence on further ideas of artificial language. I will compare his projects with Yench’s language – Idirl. An analysis of Idirl’s main assumptions will be useful to show the degree of continuation of Leibniz’s ideas in the a priori language of John Yench.

Complying with the NIH Public Access Policy - Copyright Considerations and Options

On January 11, 2008, the National Institutes of Health ('NIH') adopted a revised Public Access Policy for peer-reviewed journal articles reporting research supported in whole or in part by NIH funds. Under the revised policy, the grantee shall ensure that a copy of the author's final manuscript, including any revisions made during the peer review process, be electronically submitted to the National Library of Medicine's PubMed Central ('PMC') archive and that the person submitting the manuscript will designate a time not later than 12 months after publication at which NIH may make the full text of the manuscript publicly accessible in PMC. NIH adopted this policy to implement a new statutory requirement under which: The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law. This White Paper is written primarily for policymaking staff in universities and other institutional recipients of NIH support responsible for ensuring compliance with the Public Access Policy. The January 11, 2008, Public Access Policy imposes two new compliance mandates. First, the grantee must ensure proper manuscript submission. The version of the article to be submitted is the final version over which the author has control, which must include all revisions made after peer review. The statutory command directs that the manuscript be submitted to PMC 'upon acceptance for publication.' That is, the author's final manuscript should be submitted to PMC at the same time that it is sent to the publisher for final formatting and copy editing. Proper submission is a two-stage process. The electronic manuscript must first be submitted through a process that requires input of additional information concerning the article, the author(s), and the nature of NIH support for the research reported. NIH then formats the manuscript into a uniform, XML-based format used for PMC versions of articles. In the second stage of the submission process, NIH sends a notice to the Principal Investigator requesting that the PMC-formatted version be reviewed and approved. Only after such approval has grantee's manuscript submission obligation been satisfied. Second, the grantee also has a distinct obligation to grant NIH copyright permission to make the manuscript publicly accessible through PMC not later than 12 months after the date of publication. This obligation is connected to manuscript submission because the author, or the person submitting the manuscript on the author's behalf, must have the necessary rights under copyright at the time of submission to give NIH the copyright permission it requires. This White Paper explains and analyzes only the scope of the grantee's copyright-related obligations under the revised Public Access Policy and suggests six options for compliance with that aspect of the grantee's obligation. Time is of the essence for NIH grantees. As a practical matter, the grantee should have a compliance process in place no later than April 7, 2008. More specifically, the new Public Access Policy applies to any article accepted for publication on or after April 7, 2008 if the article arose under (1) an NIH Grant or Cooperative Agreement active in Fiscal Year 2008, (2) direct funding from an NIH Contract signed after April 7, 2008, (3) direct funding from the NIH Intramural Program, or (4) from an NIH employee. In addition, effective May 25, 2008, anyone submitting an application, proposal or progress report to the NIH must include the PMC reference number when citing articles arising from their NIH funded research. (This includes applications submitted to the NIH for the May 25, 2008 and subsequent due dates.) Conceptually, the compliance challenge that the Public Access Policy poses for grantees is easily described. The grantee must depend to some extent upon the author(s) to take the necessary actions to ensure that the grantee is in compliance with the Public Access Policy because the electronic manuscripts and the copyrights in those manuscripts are initially under the control of the author(s). As a result, any compliance option will require an explicit understanding between the author(s) and the grantee about how the manuscript and the copyright in the manuscript are managed. It is useful to conceptually keep separate the grantee's manuscript submission obligation from its copyright permission obligation because the compliance personnel concerned with manuscript management may differ from those responsible for overseeing the author's copyright management. With respect to copyright management, the grantee has the following six options: (1) rely on authors to manage copyright but also to request or to require that these authors take responsibility for amending publication agreements that call for transfer of too many rights to enable the author to grant NIH permission to make the manuscript publicly accessible ('the Public Access License'); (2) take a more active role in assisting authors in negotiating the scope of any copyright transfer to a publisher by (a) providing advice to authors concerning their negotiations or (b) by acting as the author's agent in such negotiations; (3) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License; (4) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License and also grants a license to the grantee to make certain uses of the article, including posting a copy in the grantee's publicly accessible digital archive or repository and authorizing the article to be used in connection with teaching by university faculty; (5) negotiate a more systematic and comprehensive agreement with the biomedical publishers to ensure either that the publisher has a binding obligation to submit the manuscript and to grant NIH permission to make the manuscript publicly accessible or that the author retains sufficient rights to do so; or (6) instruct NIH-funded authors to submit manuscripts only to journals with binding deposit agreements with NIH or to journals whose copyright agreements permit authors to retain sufficient rights to authorize NIH to make manuscripts publicly accessible.

Some Considerations on a Calculus with Weak References

Weak references are references that do not prevent the object they point to from being garbage collected. Most realistic languages, including Java, SML/NJ, and OCaml to name a few, have some facility for programming with weak references. Weak references are used in implementing idioms like memoizing functions and hash-consing in order to avoid potential memory leaks. However, the semantics of weak references in many languages are not clearly specified. Without a formal semantics for weak references it becomes impossible to prove the correctness of implementations making use of this feature. Previous work by Hallett and Kfoury extends λgc, a language for modeling garbage collection, to λweak, a similar language with weak references. Using this previously formalized semantics for weak references, we consider two issues related to well-behavedness of programs. Firstly, we provide a new, simpler proof of the well-behavedness of the syntactically restricted fragment of λweak defined previously. Secondly, we give a natural semantic criterion for well-behavedness much broader than the syntactic restriction, which is useful as principle for programming with weak references. Furthermore we extend the result, proved in previously of λgc, which allows one to use type-inference to collect some reachable objects that are never used. We prove that this result holds of our language, and we extend this result to allow the collection of weakly-referenced reachable garbage without incurring the computational overhead sometimes associated with collecting weak bindings (e.g. the need to recompute a memoized function). Lastly we use extend the semantic framework to model the key/value weak references found in Haskell and we prove the Haskell is semantics equivalent to a simpler semantics due to the lack of side-effects in our language.

Cryopreservation of ovarian cortex: therapeutic prospects and actuel considerations

info:eu-repo/semantics/published

Teaching yoga to seniors: essential considerations to enhance safety and reduce risk in a uniquely vulnerable age group.

BACKGROUND: Seniors age 65 and older represent the fastest-growing sector of the population and, like many Americans, are increasingly drawn to yoga. This presents both an extraordinary opportunity and a serious challenge for yoga instructors who must be both a resource and guardians of safety for this uniquely vulnerable group. A typical class of seniors is likely to represent the most diverse mix of abilities of any age group. While some may be exceedingly healthy, most fit the profile of the average older adult in America, 80% of whom have at least one chronic health condition and 50% of whom have at least two. OBJECTIVES: This article discusses the Therapeutic Yoga for Seniors program, offered since 2007 at Duke Integrative Medicine to fill a critical need to help yoga instructors work safely and effectively with the increasing number of older adults coming to yoga classes, and explores three areas that pose the greatest risk of compromise to older adult students: sedentary lifestyle, cardiovascular disease, and osteoporosis. To provide a skillful framework for teaching yoga to seniors, we have developed specific Principles of Practice that integrate the knowledge gained from Western medicine with yogic teachings.

Entorhinal cortex volume in older adults: reliability and validity considerations for three published measurement protocols.

Measuring the entorhinal cortex (ERC) is challenging due to lateral border discrimination from the perirhinal cortex. From a sample of 39 nondemented older adults who completed volumetric image scans and verbal memory indices, we examined reliability and validity concerns for three ERC protocols with different lateral boundary guidelines (i.e., Goncharova, Dickerson, Stoub, & deToledo-Morrell, 2001; Honeycutt et al., 1998; Insausti et al., 1998). We used three novice raters to assess inter-rater reliability on a subset of scans (216 total ERCs), with the entire dataset measured by one rater with strong intra-rater reliability on each technique (234 total ERCs). We found moderate to strong inter-rater reliability for two techniques with consistent ERC lateral boundary endpoints (Goncharova, Honeycutt), with negligible to moderate reliability for the technique requiring consideration of collateral sulcal depth (Insausti). Left ERC and story memory associations were moderate and positive for two techniques designed to exclude the perirhinal cortex (Insausti, Goncharova), with the Insausti technique continuing to explain 10% of memory score variance after additionally controlling for depression symptom severity. Right ERC-story memory associations were nonexistent after excluding an outlier. Researchers are encouraged to consider challenges of rater training for ERC techniques and how lateral boundary endpoints may impact structure-function associations.

Relative growth of the limbs and trunk in sifakas: heterochronic, ecological, and functional considerations.

Limb, trunk, and body weight measurements were obtained for growth series of Milne-Edwards's diademed sifaka, Propithecus diadema edwardsi, and the golden-crowned sifaka, Propithecus tattersalli. Similar measures were obtained also for primarily adults of two subspecies of the western sifaka: Propithecus verreauxi coquereli, Coquerel's sifaka, and Propithecus verreauxi verreauxi, Verreaux's sifaka. Ontogenetic series for the larger-bodied P. d. edwardsi and the smaller-bodied P. tattersalli were compared to evaluate whether species-level differences in body proportions result from the differential extension of common patterns of relative growth. In bivariate plots, both subspecies of P. verreauxi were included to examine whether these taxa also lie along a growth trajectory common to all sifakas. Analyses of the data indicate that postcranial proportions for sifakas are ontogenetically scaled, much as demonstrated previously with cranial dimensions for all three species (Ravosa, 1992). As such, P. d. edwardsi apparently develops larger overall size primarily by growing at a faster rate, but not for a longer duration of time, than P. tattersalli and P. verreauxi; this is similar to results based on cranial data. A consideration of Malagasy lemur ecology suggests that regional differences in forage quality and resource availability have strongly influenced the evolutionary development of body-size variation in sifakas. On one hand, the rainforest environment of P. d. edwardsi imposes greater selective pressures for larger body size than the dry-forest environment of P. tattersalli and P. v. coquereli, or the semi-arid climate of P. v. verreauxi. On the other hand, as progressively smaller-bodied adult sifakas are located in the east, west, and northwest, this apparently supports suggestions that adult body size is set by dry-season constraints on food quality and distribution (i.e., smaller taxa are located in more seasonal habitats such as the west and northeast). Moreover, the fact that body-size differentiation occurs primarily via differences in growth rate is also due apparently to differences in resource seasonality (and juvenile mortality risk in turn) between the eastern rainforest and the more temperate northeast and west. Most scaling coefficients for both arm and leg growth range from slight negative allometry to slight positive allometry. Given the low intermembral index for sifakas, which is also an adaptation for propulsive hindlimb-dominated jumping, this suggests that differences in adult limb proportions are largely set prenatally rather than being achieved via higher rates of postnatal hindlimb growth.(ABSTRACT TRUNCATED AT 400 WORDS)

Mapping the news on (social)-media. Methodological considerations for the analysis of local news networks.

info:eu-repo/semantics/nonPublished