The exponential growth of social data both in volume and complexity has increasingly exposed many of the shortcomings of the conventional frequentist approach to statistics. The scientific community has called for careful usage of the approach and its inference. Meanwhile, the alternative method, Bayesian statistics, still faces considerable barriers toward a more widespread application. The bayesvl R package is an open program, designed for implementing Bayesian modeling and analysis using the Stan language’s no-U-turn (NUTS) sampler. The package (...) combines the ability to construct Bayesian network models using directed acyclic graphs (DAGs), the Markov chain Monte Carlo (MCMC) simulation technique, and the graphic capability of the ggplot2 package. As a result, it can improve the user experience and intuitive understanding when constructing and analyzing Bayesian network models. A case example is offered to illustrate the usefulness of the package for Big Data analytics and cognitive computing. (shrink)

Compared with traditional statistics, only a few social scientists employ Bayesian analyses. The existing software programs for implementing Bayesian analyses such as OpenBUGS, WinBUGS, JAGS, and rstanarm can be daunting given that their complex computer codes involve a steep learning curve. In contrast, this paper introduces a new open software for implementing Bayesian network modelling and analysis: the bayesvl R package. The package aims at providing an intuitive gateway for beginners of Bayesian statistics to construct and analyse (...) mathematical models in social sciences... (shrink)

La, V. P., & Vuong, Q. H. (2019). bayesvl: Visually learning the graphical structure of Bayesian networks and performing MCMC with ‘Stan’. The Comprehensive R Archive Network (CRAN).

We show that five important elements of the ‘nomological package’— laws, counterfactuals, chances, dispositions, and counterfactuals—needn’t be a problem for the Growing-Block view. We begin with the framework given in Briggs and Forbes (in The real truth about the unreal future. Oxford studies in metaphysics. Oxford University Press, Oxford, 2012 ), and, taking laws as primitive, we show that the Growing-Block view has the resources to provide an account of possibility, and a natural semantics for non-backtracking causal counterfactuals. We (...) show how objective chances might ground a more fine-grained concept of feasibility, and furnished a places in the structure where causation and dispositions might fit. The Growing-Block view, thus understood, provides the resources to explain the close link between modality and tense, so that it predicts modal change as time passes. This account lets us capture not only what the future might hold for us, and also what might have been. (shrink)

The Random Number Generation task has a long history in neuropsychology as an assessment procedure for executive functioning. In recent years, understanding of human behavior has gradually changed from reflecting a static to a dynamic process and this shift in thinking about behavior gives a new angle to interpret test results. However, this shift also asks for different methods to process random number sequences. The RNG task is suited for applying non-linear methods needed to uncover the underlying dynamics of random (...) number generation. In the current article we present RandseqR: an R-package that combines the calculation of classic randomization measures and Recurrence Quantification Analysis. RandseqR is an easy to use, flexible and fast way to process random number sequences and readies the RNG task for current scientific and clinical use. (shrink)

This paper reconsiders certain questions about Ausonius’ two incomplete works on historical themes, Fasti and Caesares, with particular attention to points raised in a recent article by R. W. Burgess. Of the Fasti we have only a few tantalizing snippets, the packaging and not the core: what did the work look like when it left Ausonius? What was its coverage? was it in verse or prose? The Caesares as we have it breaks off in mid-quatrain, at line 139: did it (...) go beyond Elagabalus? What of the evidence in Giovanni Mansionario that Ausonius treated certain imperatores from Decius to Diocletian? (shrink)

This paper reconsiders certain questions about Ausonius’ two incomplete works on historical themes, Fasti and Caesares, with particular attention to points raised in a recent article by R. W. Burgess. Of the Fasti we have only a few tantalizing snippets, the packaging and not the core: what did the work look like when it left Ausonius? What was its coverage? was it in verse or prose? The Caesares as we have it breaks off in mid-quatrain, at line 139: did it (...) go beyond Elagabalus? What of the evidence in Giovanni Mansionario that Ausonius treated certain imperatores from Decius to Diocletian? (shrink)

Plural quantification, often used to evade Russell paradoxes, will lead back to them, given certain assumptions about propositions. This chapter provides a more generalized version of the path to paradox by showing that any theory that makes possible the construction of an appropriate packaging relation falls prey to a Russell paradox. It gives examples of widely-held metaphysical theories that require such a relation. It shows that the paradoxes that can result from plural quantification are more widely damaging, and harder to (...) tame, than has been recognized. It also displays formal requirements that any metaphysical framework with a packaging relation must meet if it is to have a chance of escaping self-contradiction. The chapter first gives the general paradox-generating setup, and then shows how three families of metaphysical assumptions allow one to instantiate it. It concludes by assessing the aftermath of the arguments presented. (shrink)

Chlorarachniophytes are amoeboflagellate, marine protists that have acquired photosynthetic capacity by engulfing and retaining a green alga. These green algal endosymbionts are severely reduced, retaining only the chloroplast, nucleus, cytoplasm and plasma membrane. The vestigial nucleus of the endosymbiont, called the nucleomorph, contains only three small linear chromosomes and has a haploid genome size of just 380 kb ‐ the smallest eukaryotic genome known. Initial characterisation of nucleomorph DNA has revealed that all chromosomes are capped with inverted repeats comprising a (...) telomere and a single ribosomal RNA operon. The nucleomorph genome is the quintessence of compactness; average space between genes is a mere 65 bp, some genes overlap, others are cotranscribed. Intense reductive pressures upon nucleomorph genes have apparently squeezed their spliceosomal‐type introns down to only 18, 19 or 20 bases in length. Studies to date indicate the nucleomorph ‐ essentially a stripped‐down eukaryotic genome ‐ encodes principally genetic housekeeping functions such as translation, transcription and splicing. (shrink)

This article investigates the claim that some truths are fundamentally or really true — and that other truths are not. Such a distinction can help us reconcile radically minimal metaphysical views with the verities of common sense. I develop an understanding of the distinction whereby Fundamentality is not itself a metaphysical distinction, but rather a device that must be presupposed to express metaphysical distinctions. Drawing on recent work by Rayo on anti-Quinean theories of ontological commitments, I formulate a rigourous theory (...) of the notion. In the final sections, I show how this package dovetails with ' interpretationist' theories of meaning to give sober content to thought that some things — perhaps sets, or gerrymandered mereological sums — can be 'postulated into existence'. (shrink)

Healthcare package decisions are complex. Different judgements about effectiveness, cost-effectiveness and disease burden influence the decision-making process. Moreover, different concepts of justice generate different ideas about fair distribution of healthcare resources. This paper presents a decision model that is used in medical school in order to familiarise medical students with the different concepts of justice and the ethical dimension of making concrete choices. The model is based on the four-stage decision model developed in the Netherlands by the Dunning Committee (...) and the discussion that followed its presentation in 1991. Having to deal with 10 medical services, students working with the model learn to discern and integrate four different ideas of distributive justice that are integrated in a flow chart: libertarian, communitarian, egalitarian and utilitarian. (shrink)

Local differences in chromatin organisation may profoundly affect the activity of eukaryotic genomes. Regulation at the level of DNA packaging requires the targeting of structural proteins and histone‐modifying enzymes to specific sites and their stable or dynamic interaction with the nucleosomal fiber. The “chromodomain”, a domain shared by many regulators of chromatin structure, has long been suspected to serve as a module mediating chromatin interactions in a variety of different protein contexts. However, recent functional analyses of a number of different (...) chromodomains revealed an unexpected diversity of interaction targets, including histones, DNA and even RNA. The chromodomains of today seem to have evolved from a common ancestral fold to fulfill various functions in different molecular contexts. Combining information gained from recent functional and structural studies of chromodomains with a bioinformatic classification of their structure could lead to the definition of sequence motifs with predictive quality for chromodomain function. BioEssays 26:133–140, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

This paper contributes to the growing social science scholarship on organic agriculture in the global South. A “boundary” framework is used to understand how negotiation among socially and geographically disparate social worlds (e.g., non-governmental organizations (NGOs), foreign donors, agricultural researchers, and small-scale farmers) has resulted in the diffusion of non-certified organic agriculture in Kenya. National and local NGOs dedicated to organic agriculture promotion, training, research, and outreach are conceptualized as “boundary organizations.” Situated at the intersection of multiple social worlds, these (...) NGOs engage in “strategic bridge building” and “strategic boundary-work.” Strategic bridge building involves the creation and use of “boundary objects” and “hybrid forms” that serve as meeting grounds for otherwise disconnected social worlds. Strategic boundary-work involves efforts to “scientize,” and thereby legitimize, organic agriculture in the eyes of foreign donors, potential research collaborators, the Kenyan state, and farmers. Examples of strategic bridge building and boundary-work are presented in the paper. The Kenyan case illustrates that different social actors can unite around a shared objective – namely, the promotion and legitimization of organic agriculture as an alternative to the Green Revolution (GR) technological package. (shrink)

I argue that irreducible multiple conceptions of moral obligation may be found in efforts to define "sustainability." Individualistic ethics currently dominate and will probably continue to shape discussions of natural resource depletion. Non-individualistic, organic ethics, which focus on entire generations of humans, are useful for overcoming problems of intergenerational identification. Finally, however, an expansion of the purview of ethics to the entire biotic community, as suggested by Aldo Leopold, represents a third scale of concern and obligation. By means of an (...) articulated, scalar bequest package, incorporating each of these disparate foci, I outline a hierarchical ethic of sustainability. (shrink)

Publicity may be considered “covert marketing” when the audience believes the message was created by an independent source rather than the product marketer. We focus on one form of publicity—video news releases —which are packaged video segments created and provided for free by a third party to the news organization. VNRs are usually shown without source disclosure. In study one, viewers’ beliefs about and perceptions of credibility in a news story are altered when they acquire persuasion knowledge about VNRs and (...) learn that the source of the story was an unedited VNR. Study two results show similar patterns despite the fact that source disclosure of the story was provided on screen. Importantly, the perceived ethics of VNRs impact perceptions of credibility. (shrink)

When the President’s Commission of 1983 concluded that there is an “ethical obligation” to secure universal access to a decent minimum of health care, some hoped that this standard would be achieved in the United States within a few years. Nearly 30 years later, when we began work on this issue of the Journal of Medicine and Philosophy (JMP), that standard had yet to be achieved, although the bills that would later become the Affordable Care Act (ACA) were then working (...) their way through Congress. Now, the ACA has been passed and signed into law. The provisions of that bill aim at achieving universal access to an “essential health benefits (EHBs) package". (shrink)

The primary goal of this article is to provide both a descriptive and comparative analysis of two representative models of systematic theology. The findings of this study show each model to be capable of processing biblical facts, packaging them into a systematic whole, and exhibiting the facts. Yet, inescapably, the conclusions inextricably connect authorial purpose to operational structure, suggesting it is necessary to reevaluate the contemporary stigmas accompanying authorial presuppositions. There is also, however, the uncovering of a potential danger area (...) within systematic theology, namely: the scientific-rational classification system, driven by cause and effect, which engenders classifications removed from Scripture. (shrink)

The DNA in a eukaryotic nucleus is packaged into a nucleosome array, punctuated by variations in the regular pattern. The local chromatin structure of inducible genes appears to fall into two categories: preset and remodeling. Preset genes are those in which the binding sites for trans‐acting factors are accessible (;i.e. in a non‐nucleosomal, DNase I hypersensitive configuration) prior to activation. In response to the activation signal, positive factors bind to cis‐acting regulatory elements and trigger transcription with no major alterations in (...) the chromatin structure of the promoter region. In contrast, remodeling genes are those in which some of the required cis‐acting regulatory elements are packaged into nucleosomes. The nucleosomes must be perturbed in response to an activation signal in order for the trans‐acting factors to gain access to cis‐acting elements; a chromatin remodeling process which forms DNase I hypersensitive sites must occur. In both cases, precise positioning of nucleosomes along the promoter region of a gene appears to be critical for appropriate regulation of expression. (shrink)

Part of the accepted scholarly lore about Kierkegaard is that he holds that “existence”—human existence—and “the System” are mutually incompatible. For Kierkegaard, human being cannot be understood in terms of a nice, neat, complete systematic package; he shows, on this view, that the Hegelian attempt to grasp all of reality in terms of a philosophical system will always fail to grasp the reality of at least one thing: the concrete, living, existing individual human being.

The aim of this study was to test the effect of face cooling with cold water vs. face cooling with neutral water during high-intensity swimming training on both the core temperature and thermal perceptions in internationally ranked long-distance swimmers during 2 randomized swimming sessions. After a standardized warm-up of 1,200 m, the athletes performed a standardized training session that consisted of 2,000 m at a best velocity then 600 m of aerobic work. Heart rate was continuously monitored during 5 × (...) 400 m, whereas Tco, thermal comfort, and thermal sensation were measured before and after each 400 m. Before and after each 400 m, the swimmers were asked to flow 200 mL of cold water or neutral water packaged in standardized bottles on their face. The swimmers were asked don’t drink during exercise. The velocity was significantly different between cold water and neutral water. The Tco was increased by ±0.5°C at race pace, under both face cooling conditions with no significant difference. No significant changes were noted in mean HR. TC was higher with Cold Cooling than Neutral Cooling and TS was lower with Cold cooling compared with Neutral cooling. The changes in perceptual parameters caused by face cooling with cold water reflect the psychological impact on the physical parameters. The mean velocity was less important with face cooling whereas the heat rate and Tco were the same in the both conditions. The mechanism leading to these results seems to involve brain integration of signals from physiological and psychological sources. (shrink)

(The Kindle book can be ordered for $3.21 from Amazon) -/- Thinking is a fundamental activity of our species – those that give names to other creatures and call themselves humans. Textbooks tell us that there is about 1.2 kg of matter called the brain inside the human body. It sounds small but actually is proportionally the biggest among all animals on Earth. -/- I became more aware of thinking at around 5th grade upon hearing about an ancient paradox. It (...) can be summarized as follows. -/- ¤ -/- Once upon a time, there was a stupid king. In his kingdom lived a sage who was highly respected for his intelligence. The King did not appreciate this fact. Maybe the Sage made fun of the King’s intellect, but I am not so sure. Anyway, one day, the King summoned the Sage, intending to kill him. -/- The King said, “Wise man, I heard you earn a living by thinking and arguing. Now I give you two options to die.” -/- The Sage said, “Please tell me the choices, Your Majesty.” -/- The King continued, “You live by your tongue, so I will let you say one sentence before you die. If what you say is true, you will die by hanging. If what you say is false, you will die by beheading.” -/- Little did the King know that this was a stupid order. After a short while, the Sage confidently spoke his “last words”, which actually were what saved his life: -/- “Your Majesty, I am about to be beheaded!” -/- ¤ -/- As a “wild animal” going out into life from a young age, my brain spent a lot of time and energy looking for food. Now that I have become older, my body no longer needs so much sustenance. However, my mind craves a different type of nourishment: food for thought. -/- Food for thought can directly lead to food (on the table). My main job as a scientist exemplifies what I have just stated. Maybe we were wrong. Maybe it has been “thought for food” all along, like in such a sequence as TFFTTTFTFFTTFFFT... -/- In the hyper-chaotic infosphere today, we are surrounded by the noises of information, not only as wavy shores or waterfalls but also mega-tsunamis, through Twitter, Facebook, Tiktok, Instagram, Youtube, etc. More than ever, tranquility and calmness are necessary. Like what you have seen in wilderness video clips, predators such as lions, bears, and alligators act lightning-fast when catching prey. But when food is served, the natural world returns to its peaceful, soothing silence. -/- This short book is in its own tidy infosphere, where each little story is also brief and self-contained. Despite this small appearance, I hope the content inside carries the value of tranquility and life observation. The book is petite, but pretty sure not malnourished. A not-too-small detail is that the way the content was shaped and distilled reflects some innovations of mine and my research team: the mindsponge theory, a new theory of serendipity, the bayesvl R package, the BMF analytics, as well as other experiences from working in the field of science. After all, scientific works were my main source of food (before this book sells well – if it does). -/- Welcome to the priceless sober moments – with a chicken-burger price tag! -/- I hope this book will bring readers some moments of calmness, peaceful smiles, and maybe a couple of good laughs too. -/- ~~~ -/- *This update: December 12, 2023 (Third edition, with additions). (shrink)

This research employs the Bayesian network modeling approach, and the Markov chain Monte Carlo technique, to learn about the role of lies and violence in teachings of major religions, using a unique dataset extracted from long-standing Vietnamese folktales. The results indicate that, although lying and violent acts augur negative consequences for those who commit them, their associations with core religious values diverge in the final outcome for the folktale characters. Lying that serves a religious mission of either Confucianism or Taoism (...) (but not Buddhism) brings a positive outcome to a character (βT_and_Lie_O= 2.23; βC_and_Lie_O= 1.47; βT_and_Lie_O= 2.23). A violent act committed to serving Buddhist missions results in a happy ending for the committer (βB_and_Viol_O= 2.55). What is highlighted here is a glaring double standard in the interpretation and practice of the three teachings: the very virtuous outcomes being preached, whether that be compassion and meditation in Buddhism, societal order in Confucianism, or natural harmony in Taoism, appear to accommodate two universal vices—violence in Buddhism and lying in the latter two. These findings contribute to a host of studies aimed at making sense of contradictory human behaviors, adding the role of religious teachings in addition to cognition in belief maintenance and motivated reasoning in discounting counterargument. (shrink)

Working in academia is challenging, even more so for those with limited resources and opportunities. Researchers around the world do not have equal working conditions. The paper presents the structure, operation method, and conceptual framework of the SM3D Portal's community coaching method, which is built to help Early Career Researchers (ECRs) and researchers in low-resource settings overcome the obstacle of inequality and start their career progress. The community coaching method is envisioned by three science philosophies (cost-effectiveness, transparency spirit, and proactive (...) attitude) and established and operated based on the Serendipity-Mindsponge-3D knowledge (SM3D) management framework (i.e., mindsponge thinking and Bayesian Mindsponge Framework analytics serve as the coaching program's foundational theory and analytical tools). The coaching method also embraces Open Science's values for lowering the cost of doing science and encouraging the trainees to be transparent, which is expected to facilitate the self-correcting mechanism of science through open data, open review, and open dialogue. Throughout the training process, members are central beneficiaries by gaining research knowledge and skills, acquiring publication as the training's product, and shifting their mindsets from “I can't do it” to “I can do it,” and at the same time transforming a mentee to be ready for a future mentor's role. The coaching method is thus one of the members, for the member, by the members. -/- • The paper provides the structure, operation method, and conceptual framework of the SM3D Portal's community coaching method, which is built to help Early Career Researchers (ECRs) and researchers in low-resource settings overcome the obstacle of inequality and start their career progress. • The paper presents three major science philosophies envisioning the establishment and operation of scholarly community coaching. • The paper employs the mindsponge theory and BMF analytics to construct a conceptual framework explaining how an environment is created to help shift members’ mindsets from “I can't do it” to “I can do it.”. (shrink)

Being a researcher is challenging, especially in the beginning. Early Career Researchers (ECRs) need achievements to secure and expand their careers. In today’s academic landscape, researchers are under many pressures: data collection costs, the expectation of novelty, analytical skill requirements, lengthy publishing process, and the overall competitiveness of the career. Innovative thinking and the ability to turn good ideas into good papers are the keys to success.

Academia is a competitive environment. Early Career Researchers (ECRs) are limited in experience and resources and especially need achievements to secure and expand their careers. To help with these issues, this book offers a new approach for conducting research using the combination of mindsponge innovative thinking and Bayesian analytics. This is not just another analytics book. 1. A new perspective on psychological processes: Mindsponge is a novel approach for examining the human mind’s information processing mechanism. This conceptual framework is used (...) to construct models in studies. The framework is highly flexible and widely applicable for many different types of information processes. The mindsponge approach can help researchers discover interesting ideas or even formulate their very own theories when investigating psychosocial phenomena. This approach brings a fresh wind to the current landscape of social sciences and humanities (SSH). 2. Easy-to-follow analysis protocol: The Bayesian Mindsponge Framework (BMF analytics) is useful in terms of computing and visualizing power but also easy to learn and apply. Contrary to being intimidating, the Bayesian analytics section of this book is presented in a reader-friendly manner with a detailed yet clear step-by-step procedure. Examples are from published BMF articles, allowing readers to immediately practice the method and quickly create their own applications. With educational purposes in mind, the book is very suitable for ECRs who are looking to innovate their research methods. 3. Advocating for low-cost, high-quality research: Doing science can be very costly. Mindsponge innovative thinking and BMF analytics help produce impactful studies using openly available data on online repositories. This is based on the authors’ previous works and experiences. The book presents examples of employing the open R package bayesvl on secondary data from different sources. With less financial constraints, researchers can have more freedom of thought to pursue their curiosity and creativity. ECRs in low- and middle-income countries may find this aspect crucial in their careers. 4. Support and collaboration: The authors share their insights from experiences in the academic publishing system to help readers get through the processes of manuscript writing and peer-reviewing more easily. The authors are also ready to support other researchers with further inquiries and collaboration opportunities at the following website, mindsponge(dot)info. This book is for: a) ECRs whose only abundant resources are their innovation capacity and strength of will; b) Researchers in SSH who want to explore a novel approach to thinking and study conducting; c) Low- and middle-income countries’ researchers looking for a cost-effective research protocol; and, d) Innovative thinkers who want to turn their interesting thoughts into good publications. (shrink)

Cross-classified random effects models have been developed for appropriately analyzing data with a cross-classified structure. Despite its flexibility and the prevalence of cross-classified data in social and behavioral research, CCREMs have been under-utilized in applied research. In this article, we present CCREMs as a general and flexible modeling framework, and present a wide range of existing models designed for different purposes as special instances of CCREMs. We also introduce several less well-known applications of CCREMs. The flexibility of CCREMs allows these (...) models to be easily extended to address substantive questions. We use the free R package PLmixed to illustrate the estimation of these models, and show how the general language of the CCREM framework can be translated into specific modeling contexts. (shrink)

Researchers in the fields of sign language and gesture studies frequently present their participants with video stimuli showing actors performing linguistic signs or co-speech gestures. Up to now, such video stimuli have been mostly controlled only for some of the technical aspects of the video material, leaving open the possibility that systematic differences in video stimulus materials may be concealed in the actual motion properties of the actor’s movements. Computer vision methods such as OpenPose enable the fitting of body-pose models (...) to the consecutive frames of a video clip and thereby make it possible to recover the movements performed by the actor in a particular video clip without the use of a point-based or markerless motion-tracking system during recording. The OpenPoseR package provides a straightforward and reproducible way of working with these body-pose model data extracted from video clips using OpenPose, allowing researchers in the fields of sign language and gesture studies to quantify the amount of motion pertaining only to the movements performed by the actor in a video clip. These quantitative measures can be used for controlling differences in the movements of an actor in stimulus video clips or, for example, between different conditions of an experiment. In addition, the package also provides a set of functions for generating plots for data visualization, as well as an easy-to-use way of automatically extracting metadata from large sets of video files. (shrink)

Розкрито сутність поняття «рейтинг». Доведено значущість рейтингової оцінки для суб’єктів фінансового ринку, зокрема для страхових компаній, потенційних страхувальників, інвесторів та кредиторів.

"Williams's masterful translation satisfies (at last!) a long-standing need. There are lots of good translations of Augustine's great work, but until now we have been forced to choose between those that strive to replicate in English something of the majesty and beauty of Augustine's Latin style and those that opt instead to convey the careful precision of his philosophical terminology and argumentation. Finally, Williams has succeeded in capturing both sides of Augustine's mind in a richly evocative, impeccably reliable, elegantly readable (...) presentation of one of the most impressive achievements in Western thought--Augustine's Confessions." --Scott MacDonald, Professor of Philosophy and Norma K. Regan Professor in Christian Studies, Cornell University. (shrink)

R.I.G Hughes offers the first detailed and accessible analysis of the Hilbert-space models used in quantum theory and explains why they are so successful.

In this first paperback edition, a new introduction by Tom Burke establishes the ongoing importance of Sleeper's analysis of the integrity of Dewey's work and ...