Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions

If we are to plan conservation strategies that minimize the loss of evolutionary history through human–caused extinctions, we must understand how this loss is related to phylogenetic patterns in current extinction risks and past speciation rates. Nee & May (1997, Science 278, 692–694) showed that for a randomly evolving clade (i) a single round of random extinction removed relatively little evolutionary history, and (ii) extinction management (choosing which taxa to sacrifice) offered only marginal improvement. However, both speciation rates and extinction risks vary across lineages within real clades. We simulated evolutionary trees with phylogenetically patterned speciation rates and extinction risks (closely related lineages having similar rates and risks) and then subjected them to several biologically informed models of extinction. Increasing speciation rate variation increases the extinction–management pay–off. When extinction risks vary among lineages but are uncorrelated with speciation rates, extinction removes more history (compared with random trees), but the difference is small. When extinction risks vary and are correlated with speciation rates, history loss can dramatically increase (negative correlation) or decrease (positive correlation) with speciation rate variation. The loss of evolutionary history via human–caused extinctions may therefore be more severe, yet more manageable, than first suggested.
Time Course of Motor Preparation during Visual Search with Flexible Stimulus–Response Association

Whether allocation of visuospatial attention can be divorced from saccade preparation has been the subject of intense research efforts. A variant of the visual search paradigm, in which a feature singleton indicates that the correct saccade should be directed to it (prosaccade) or to the opposite distractor (antisaccade), has been influential in addressing this core topic. We performed a causal assessment of this controversy by delivering an air puff to one eye to invoke the trigeminal blink reflex as monkeys performed this visual search task. Blinks effectively remove saccadic inhibition and prematurely trigger impending saccades in reaction time tasks, thus providing a behavioral readout of the premotor plan. We found that saccades accompanied blinks during the initial allocation of attention epoch and that these movements were directed to the singleton for both prosaccade and antisaccade trials. Blinks evoked at later times were accompanied with saccades to the correct end point location: the singleton on prosaccade trials and the opposite distractor on antisaccade trials. These results provide support for concurrent encoding of visuospatial attention and saccade preparation during visual search behavior.
Patterns and Correlates of Discontinuation of the Initial HAART Regimen in an Urban Outpatient Cohort

Objectives To describe the patterns and correlates of discontinuation of the initial highly active antiretroviral therapy (HAART) regimen in an urban, outpatient cohort of antiretroviral-naive patients. Design Retrospective cohort of 345 randomly selected antiretroviral-naive patients who initiated HAART on 6 selected regimens between January 1997 and May 2001 in New Orleans, LA. Methods An investigator reviewed medical records to collect information on concurrent medications, symptoms/diagnoses, staging indicators, and reasons for HAART discontinuation. Proportional hazards regression methods were used to identify predictors of discontinuation. Results After a median follow-up of 8.1 months, 61% of patients changed or discontinued their initial HAART regimen; 24% did so because of an adverse event. The events most commonly cited as the cause for discontinuation were nausea, vomiting, and diarrhea. A detectable viral load was associated with discontinuation at any time, while reporting nausea/vomiting or dizziness at the previous visit were associated with discontinuation during the first 3 months on HAART. Nausea/vomiting and not having AIDS at the time of HAART initiation were associated with discontinuation due to an adverse event at any time, while a high viral load, and dizziness or anorexia/weight loss at the previous visit were associated with discontinuation due to an adverse event in the first 3 months on HAART. Conclusions Gastrointestinal adverse events of HAART are the most frequently cited reason for discontinuation of HAART. An effort should be made to educate patients about these events and to encourage continued adherence. Additionally, appropriate prophylaxes for these events are warranted.
Enabling view-dependent stereoscopic projection in real environments

We show how view-dependent image-based and geometric warping, radiometric compensation, and multi-focal projection enable a view-dependent stereoscopic visualization on ordinary (geometrically complex, colored and textured) surfaces within everyday environments. Special display configurations for immersive or semi-immersive AR/VR applications that require permanent and artificial projection canvases might become unnecessary. We demonstrate several ad-hoc visualization examples in a real architectural and museum application context.
Natural History of Venous Thromboembolism

Most deep vein thromboses (DVTs) start in the calf; however, thrombi that remain confined to the calf rarely cause leg symptoms or are associated with symptomatic pulmonary embolism (PE). The probability that calf DVT will extend to involve the proximal veins, and subsequently cause PE, increases with the severity of the initiating prothrombotic stimulus and if this stimulus persists. Although acute venous thromboembolism (VTE) usually presents with either leg or pulmonary symptoms, most patients have thrombosis at both sites at the time of diagnosis. Treated proximal DVTs resolve slowly, and half of patients still have detectable thrombi after a year. About 10% of patients with symptomatic DVT develop severe postthrombotic syndrome within 5 years. This is more likely to occur if there has been an ipsilateral recurrent DVT. About 10% of PEs are rapidly fatal. Of PEs that are diagnosed before death, about 50% are associated right ventricular dysfunction, a finding that is associated with a high short-term mortality. There is about 50% resolution of PE after 1 month of treatment, and perfusion eventually returns to normal in two thirds of patients. After a course of treatment, the risk of recurrent thrombosis is higher in patients without a reversible risk factor and in those with certain biochemical abnormalities, including antiphospholipid antibodies, hyperhomocysteinemia, and homozygous factor V Leiden.
Safety leadership: A longitudinal study of the effects of transformational leadership on safety outcomes

Transformational leadership based interventions were assessed using a pre-test, post-test, and control group design. Leaders (N=54) from 21 long-term health care organizations were randomly assigned to general transformational leadership training, safety-specific transformational leadership training, or a control group. Multivariate analysis of variance (MANOVA) showed that leadership training resulted in significant effects on manager post-training ratings of safety attitudes, intent to promote safety, and self-efficacy. The effects of leadership training on employee (N=115) perceptions of leader safety-specific transformational leadership, safety climate, safety participation, safety compliance, safety-related events and, injuries were also assessed. Multivariate analysis of covariance (MANCOVA), with the pre-test scores as the covariates, showed that leadership training resulted in significant effects on the safety-specific transformational leadership and safety climate outcomes.
Analytical force calculation in brushless-dc motors II: Mathematical details of the alternative approach

Expanding Part I of our contribution, this paper deals with the analytical calculation of the tangential forces in brushless dc machines, where we extend previously developed methods using conformal mapping and the Maxwell stress theory to enable a greater applicability of such methods. While Part I focuses on the explanation of the methodology itself, aiming to convey the overall picture and not to obscure the message with lengthy developments of formulae, this present Part II provides the detailed developments of the different expressions that are important for those to carry out further research in this area.
PRISM: platform for remote sensing using smartphones

To realize the potential of opportunistic and participatory sensing using mobile smartphones, a key challenge is ensuring the ease of developing and deploying such applications, without the need for the application writer to reinvent the wheel each time. To this end, we present a Platform for Remote Sensing using Smartphones (PRISM) that balances the interconnected goals of generality, security, and scalability. PRISM allows application writers to package their applications as executable binaries, which offers efficiency and also the flexibility of reusing existing code modules. PRISM then pushes the application out automatically to an appropriate set of phones based on a specified set of predicates. This push model enables timely and scalable application deployment while still ensuring a good degree of privacy. To safely execute untrusted applications on the smartphones, while allowing them controlled access to sensitive sensor data, we augment standard software sandboxing with several PRISM-specific elements like resource metering and forced amnesia. We present three applications built on our implementation of PRISM on Windows Mobile: citizen journalist, party thermometer, and road bump monitor. These applications vary in the set of sensors they use and in their mode of operation (depending on human input vs. automatic). We report on our experience from a small-scale deployment of these applications. We also present a large-scale simulation-based analysis of the scalability of PRISM's push model.
Interpretive sensory-access theory and conscious intentions

It is typically assumed that while we know other people's mental states by observing and interpreting their behavior, we know our own mental states by introspection, i.e., without interpreting ourselves. In his latest book, The opacity of mind: An integrative theory of self-knowledge, Peter Carruthers [2011. The opacity of mind: An integrative theory of self-knowledge. Oxford: Oxford University Press] argues against this assumption. He holds that findings from across the cognitive sciences strongly suggest that self-knowledge of conscious propositional attitudes such as intentions, judgments, and decisions involves a swift and unconscious process of self-interpretation that utilizes the same sensory channels that we employ when working out other people's mental states. I provide an overview of Carruthers’ book before discussing a pathological case that challenges his account of self-knowledge and mentioning empirical evidence that undermines his use of a particular kind of data in his case against introspection of conscious attitudes.
Trial suggests yoga and exercise lead to modest improvements in menopause-related quality of life: longer term studies are needed

Commentary on: Reed SD, Guthrie KA, Newton KM, et al. Menopausal quality of life: RCT of yoga, exercise, and omega-3 supplements. Am J Obstet Gynecol 2014;210:244.e1–11. [OpenUrl][1][CrossRef][2] Since publication of the Women's Health Initiative Study, the potential benefits of non-pharmacological therapies for menopause-related symptoms have gained increased interest among midlife women, clinicians and researchers.1 Interventions requiring behavioural change have yielded mixed outcomes, owing to small sample sizes, a variety of outcome measures, lack of control groups and limited follow-up.2–4 To assess the effects of exercise, yoga and ω-3 therapy on menopause-specific quality of life, MS-FLASH investigators conducted a multisite factorial design (3×2), randomised controlled trial in which women were randomised to 12 weeks of exercise, yoga or usual activity and simultaneously randomised to receive ω-3 supplements … [1]: {openurl}? query=rft.jtitle%253DAm%2BJ%2BObstet%2BGynecol%26rft.volume%253D210%26rft.spage%253D244.e1%26rft_id%253Dinfo%253Adoi%252F10.1016%252Fj.ajog. 2013.11. 016%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [2]: /lookup/external-ref? access_num=10.1016/j.ajog. 2013.11. 016&link_type=DOI
The Paradox of Social Class and Sports Involvement

Studies in the sociology of sport have found that the higher one's social class, the greater is one's overall involvement in sports, but the less likely is one's involvement in what have come to be called `prole' sports. Using data from the 1993 General Social Survey, this study tests two explanations for this paradox, one stressing class-based differences in cultural capital and the other emphasizing class-based differences in economic capital. Findings show that those who are richest in cultural capital and those richest in economic capital are most likely to be involved in sports generally, and that these tendencies are independent of one another. However, those richest in cultural capital are least likely to be involved in `prole' sports, and economic capital has no bearing on `prole' sports involvement. In all, cultural capital explains the paradox of social class and sports involvement better than economic capital does. Inferences are drawn for the role of sports involvement in the reproduction of social inequality, and for the `cultural omnivore' thesis.
Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin

Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT) using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through “walking” in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A “walking. ”
Liberating the Markets for Journal Publications: Some Specific Options

While I have great sympathy for the views put forward in the paper by Macdonald and Kam (2007), I feel that their picture of current publication practices in management studies is just a little too bleak. It relies rather too much on extreme examples, old references and publication in other disciplines. However there are two key related themes in the paper that certainly deserve further attention. Firstly, the virtuous/vicious circles in journal publication that, on the one hand, guarantee quality and on the other can lead to stagnation in a discipline, and secondly, the role that reviewing plays in these processes. While I agree that their deeply unserious Tinkerbell solution maintains the nursery metaphor, it makes no serious effort to offer any alternative solutions to the problems they have identified. I want to argue that academic journal publication can usefully be analysed as a market system based upon exchanges, through which value is created and distributed through processes of evaluation. Further complexity is created since this primary market is also embedded in the commercial journal publication market and strongly linked to the academic labour market. However as a result of changes in technology and, increasingly, in the attitudes of academic communities, alternative market forms involving open publishing and open peer review become possible. In what follows the nature of this market will be described, new options suggested and their viability assessed.
Research on Parallel Symbolic Execution through Program Dependence Analysis

Through program dependence analysis, the method of parallel symbolic execution based on reduction about program execution path family was proposed. Firstly, instruction statements which affect on the symbolic value were extracted according to data dependency. then the key branch conditions controlling these statements were located and connected. Thus the reduction algorithm from multiple paths of which symbolic values are all the same to path families was was designed and implemented. Finally, path family chain was built and parallel symbolic execution was realized. the experimental results show that the method promotes parallel processing ability and test efficiency, compared with common parallel scheduling policy of allocating program execution path.
Two galantamine titration regimens in patients switched from donepezil

Engedal K, Davis B, Richarz U, Han J, Schäuble B, Andreasen N. Two galantamine titration regimens in patients switched from donepezil. Acta Neurol Scand: 2012: 126: 37–44. © 2011 John Wiley & Sons A/S.
Into the Dark Domain: The UK Web Archive as a Source for the Contemporary History of Public Health

With the migration of the written record from paper to digital format, archivists and historians must urgently consider how web content should be conserved, retrieved and analysed. The British Library has recently acquired a large number of UK domain websites, captured 1996–2010, which is colloquially termed the Dark Domain Archive while technical issues surrounding user access are resolved. This article reports the results of an invited pilot project that explores methodological issues surrounding use of this archive. It asks how the relationship between UK public health and local government was represented on the web, drawing on the ‘declinist’ historiography to frame its questions. It points up some difficulties in developing an aggregate picture of web content due to duplication of sites. It also highlights their potential for thematic and discourse analysis, using both text and image, illustrated through an argument about the contradictory rationale for public health policy under New Labour.
Diachronic Explanations of Sound Patterns

Phonological systems show clear signs of being shaped by phonetics. Sound patterns are overwhelmingly phonetically 'natural', in that they reflect the influence of physical constraints on speech production and perception, and categorical phonological processes often mirror low-level gradient phonetic effects. The question of how best to explain and model the influence of phonetics on phonology has been approached in different ways, one of which situates the locus of explanation in the diachronic domain of language change, in particular sound change. On this view, recurrent sound patterns merely reflect recurrent sound changes with phonetic origins, typically in speech perception. Explicit models of sound change are reviewed and illustrated, in particular Ohala's listener-based model and Blevins' Evolutionary Phonology framework, and the relevance of exemplar-based models of speech production and perception is also noted. Current issues of controversy regarding the adequacy of diachronic vs. synchronic explanations for the typology of sound patterns are surveyed. 1. Introduction: the phonetic bases of phonology As even a cursory acquaintance with phonology will reveal, the vast majority of sound patterns and phonological processes in the world's languages show clear indications of being shaped by the physical constraints of speech production and perception. Much of phonology is thus arguably 'natural' from a phonetic perspective. Distributional patterns and asymmetries in the ability of different positions to support phonemic contrasts (syllable onset vs. coda, stressed vs. unstressed syllable) are strongly correlated with the relative salience of acoustic- perceptual cues and/or the relative magnitude of articulatory gestures in the positions in question. Common phonological processes usually have clear parallels in low-level patterns of phonetic variation, both in the articulatory domain (coarticulation, gestural undershoot, inter-gestural timing and overlap, boundary strengthening) and in the acoustic-perceptual domain (confusion, misperception; aerodynamic effects on the acoustic signal). Such obvious and pervasive correlations raise a number of questions which cut to the conceptual core of phonology as a discipline. What is the nature of the connection between phonetic 'substance' and the higher-order patterning that phonology deals with? How close is this connection, and how—if at all—should we allow it to inform our theoretical models of the implicit knowledge speakers have of the sound patterns of their native language? To what extent, and in what manner, should phonetics be called upon to explain empirical generalizations about the typology of sound patterns and phonological systems? What bearing does all of this have on the question of
White Racial Reasoning: Rational Racism in the Perceptions of White Males

Dans cet article, l'A se penche sur le raisonnement en terme de race aux Etats-Unis. L'A analyse ici les perceptions et les constructions de l'identite fondee sur la rapport Noir/Blanc et du concept de colorblindess, de neuf hommes blancs de la region de la Nouvelle Orleans, pour tenter de comprendre le glissment idelogique entre race et racisme
Symmetry Breaking with Noisy Processes

Biology and computer science intersect at the problem of symmetry breaking, which is relevant in both fields. Accordingly, in recent years, distributed algorithm theorists have studied symmetry breaking problems in models inspired by biology to help provide insight into the capabilities and constraints of this natural process. A potential shortcoming of these models, however, is that they execute distributed algorithms precisely as specified. In nature, where computation is often implemented by messy analog systems, this precision cannot necessarily be guaranteed. Motivated by this observation, in this paper we present a general method for injecting computational noise into any distributed system model that describes processes as interacting state machines. Our method captures noise as a force that can cause state machines to transition to the wrong state. We combine this formalization of noise with the beeping models that have been a popular target of recent work on bio-inspired symmetry breaking. We produce new upper and lower bounds for both single hop and multihop models---studying leader election in the former and the maximal independent set problem in the latter. These bounds introduce new techniques for achieving robustness to noise, and identify some fundamental limits in this pursuit. We argue that both our general approach and specific results can help advance the productive relationship between biology and algorithm theory.