SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases

Approximating Fractional Time Quantum Evolution

An algorithm is presented for approximating arbitrary powers of a black box unitary operation, $\mathcal{U}^t$, where $t$ is a real number, and $\mathcal{U}$ is a black box implementing an unknown unitary. The complexity of this algorithm is calculated in terms of the number of calls to the black box, the errors in the approximation, and a certain `gap' parameter. For general $\mathcal{U}$ and large $t$, one should apply $\mathcal{U}$ a total of $\lfloor t \rfloor$ times followed by our procedure for approximating the fractional power $\mathcal{U}^{t-\lfloor t \rfloor}$. An example is also given where for large integers $t$ this method is more efficient than direct application of $t$ copies of $\mathcal{U}$. Further applications and related algorithms are also discussed.Comment: 13 pages, 2 figure

Aspek Medikolegal Tatalaksana Kematian Di Kota Manado

: Birth, morbidity and death are data that will be needed to make a life table. Life table is very valuable information that will be needed in making decision and regulation in health and medical field. Regulations based on valid data will give huge amount of benefit for the advancement of health and medical field at Indonesia, especially in Manado. Death and cause of death certification is part of doctor\u27s responsibility that has a big effect on relative\u27s law status and so it must be handled properly. Death and cause of death registration could also detect any unnatural death occuring outside the health facility so it can be handled properly by the police. Death and cause of death medicolegal protocol in turn could help us upholding the law by apprehanding criminals that are trying to eliminate biological evidence

Biomechanical analysis of the penalty-corner drag-flick of elite male and female hockey players

The aim of this study was to analyse the kinematic sequencing in the penalty-corner drag-flicks of elite male and female field hockey players of international calibre. Thirteen participants (one skilled male drag-flicker and six male and six female elite players) participated in the study. An optoelectronic motion analysis system was used to capture the drag-flicks with six cameras, sampling at 250 Hz. Select ground reaction force parameters were obtained from a force platform which registered the last support of the front foot. Twenty trials were captured from each subject. Both player groups showed significantly (p < 0.05) smaller ball velocity at release, peak angular velocity of the pelvis, and negative and positive peak angular velocities of the stick than the skilled subject. Normalised ground reaction forces of the gender groups were also smaller than that of the skilled drag-flicker. By comparing these players we established that the cues of the skill level are a wide stance, a whipping action (rapid back lift) of the stick followed by an explosive sequential movement of the pelvis, upper trunk and stick

Design activism: catalysing communities of practice

Over the last decade, we have witnessed renewed interest in design as a socially engaged practice. Much of the debates around ‘social design’ point towards myriad approaches and disciplinary fields interwoven with grass-roots initiatives and social movements. Among these, design activism has gained traction as critical spatial practice that operates on the fringes of commercial and institutional spheres. The temporal, spatial and experimental nature of design activism is well delineated in scholarship but its long-term effect on everyday urban environments remains elusive. Moreover, the influence of design activism on socio-spatial dynamics is indeed largely under researched. By mobilising social practice theory, this paper proposes a novel theorisation of design activism that sheds light on the social formations and collective practices catalysed through the activist impulse. This ontological shift embraces an understanding of the socio-material world through practice. Such characterisation of design activism underscores collective moments of integration of the constitutive elements of practice, encapsulated by Shove, Pantzar and Watson as ‘material, competence and meaning’. The authors' own empirical research, funded by the Economic and Social Research Council (ESRC) in the UK, reveals design activism as necessarily intertwined with other everyday practices – gardening, celebrating, playing – that coalesce around a shared sense of citizenship. It also advances the role of design activism in forging communities of practice: mutually supportive and self-sustaining groups emerging out of the personal relations sustained and organised around a practice of place making

Fenham Pocket Park: a holding ground

Fenham Pocket Park (FPP) is a community-led urban space, founded in 2016 in a context of austerity imposed by the British Government. Beginning as a University-third-sector collaboration, the project transformed an undefined soulless space between a swimming pool and a library into a place for exchange, dwelling and celebrating. It also gave rise to a residents’ group, the Friends of Fenham Pocket Park (FFPP), who became custodians of the space and committed to developing it further. Six years on, the area has suffered further from the impact of austerity and retreat of public services, and the FFPP group has experienced setbacks and a lull in participation. This study documents, through student journals and participant observation, the role played by BA Architecture-and-Urban- Planning students in re-charging the project through playful creative practice interventions and dialogue with residents. It explores the entanglement of civil society with students in a process that is framed by Freire’s critical pedagogy and recent scholarship on lively materials. Here, making is theorised as a vehicle through which pedagogies of hope can embed themselves in the community. The paper thus meditates on the agency of emplaced student-led making in (re)kindling community action, creating collectively shaped social and climate futures

Oct4 Is a Key Regulator of Vertebrate Trunk Length Diversity

The deposited article version is a post-print version (final draft post-refereeing) and included supplementary information.Vertebrates exhibit a remarkably broad variation in trunk and tail lengths. However, the evolutionary and developmental origins of this diversity remain largely unknown. Posterior Hox genes were proposed to be major players in trunk length diversification in vertebrates, but functional studies have so far failed to support this view. Here we identify the pluripotency factor Oct4 as a key regulator of trunk length in vertebrate embryos. Maintaining high Oct4 levels in axial progenitors throughout development was sufficient to extend trunk length in mouse embryos. Oct4 also shifted posterior Hox gene-expression boundaries in the extended trunks, thus providing a link between activation of these genes and the transition to tail development. Furthermore, we show that the exceptionally long trunks of snakes are likely to result from heterochronic changes in Oct4 activity during body axis extension, which may have derived from differential genomic rearrangements at the Oct4 locus during vertebrate evolution.Fundação para a Ciência e a Tecnologia grants: ( PTDC/BEX-BID/0899/2014, SFRH/BD/51876/2012); Santa Casa da Misericordia de Lisboa grant: (SCML-MC-60-2014); Howard Hughes Medical; HHMI international graduate student research fellowship.info:eu-repo/semantics/publishedVersio

Larger visual changes compress time: The inverted effect of asemantic visual features on interval time perception; 35316292

Time perception is fluid and affected by manipulations to visual inputs. Previous literature shows that changes to low-level visual properties alter time judgments at the millisecond-level. At longer intervals, in the span of seconds and minutes, high-level cognitive effects (e.g., emotions, memories) elicited by visual inputs affect time perception, but these effects are confounded with semantic information in these inputs, and are therefore challenging to measure and control. In this work, we investigate the effect of asemantic visual properties (pure visual features devoid of emotional or semantic value) on interval time perception. Our experiments were conducted with binary and production tasks in both conventional and head-mounted displays, testing the effects of four different visual features (spatial luminance contrast, temporal frequency, field of view, and visual complexity). Our results reveal a consistent pattern: larger visual changes all shorten perceived time in intervals of up to 3min, remarkably contrary to their effect on millisecond-level perception. Our findings may help alter participants'' time perception, which can have broad real-world implications

Early development of the malleus and incus in humans.

It is widely accepted by developmental biologists that the malleus and incus of the mammalian middle ear are first pharyngeal arch derivatives, a contention based originally on classical embryology that has now been backed up by molecular evidence from rodent models. However, it has been claimed in several studies of human ossicular development that the manubrium of the malleus and long process of the incus are actually derived from the second arch. This 'dual-arch' interpretation is commonly presented in otolaryngology textbooks, and it has been used by clinicians to explain the aetiology of certain congenital abnormalities of the human middle ear. In order to re-examine the origins of the human malleus and incus, we made three-dimensional reconstructions of the pharyngeal region of human embryos from 7 to 28 mm crown-rump length, based on serial histological sections from the Boyd Collection. We considered the positions of the developing ossicles relative to the pharyngeal pouches and clefts, and the facial and chorda tympani nerves. Confirming observations from previous studies, the primary union between first pharyngeal pouch and first cleft found in our youngest specimens was later lost, the external meatus developing rostroventral to this position. The mesenchyme of the first and second arches in these early embryos seemed to be continuous, but the boundaries of the developing ossicles proved to be very hard to determine at this stage. When first distinguishable, the indications were that both the manubrium of the malleus and the long process of the incus were emerging within the first pharyngeal arch. We therefore conclude that the histological evidence, on balance, favours the 'classical' notion that the human malleus and incus are first-arch structures. The embryological basis of congenital ossicular abnormalities should be reconsidered in this light.This is the author accepted manuscript. The final version is available from Wiley via https://doi.org/10.1111/joa.1252