The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Hui Shi (370-310B.C.E.?) is a unique one among the pre-Qin scholars. The object and orientation of his scholarship emphasized on “chasing after the materials” or the research for objective knowledge of natural things. He shows a tendency of tolerating and advocating diversity and variety, and intentionally pursuing new and unusual ideas. In certain degree he judges the value of knowledge by its truthfulness rather than its usefulness. As pointed out by Wing-tsit Chan, Hui shi represents a “tendency in ancient China (...) toward intellectualism for its own sake”. (shrink)

I present a developmental account of Aristotle’s concept of hê hylê (usually translated “the matter”), focused the earliest developments. I begin by analyzing fragments of some lost early works and a chapter of the Organon, texts which indicate that early in his career Aristotle had not yet begun to use he hylê in a technical sense. Next, I examine Physics II 3, a chapter in which Aristotle conceives of he hylê not as a kind of cause in its own right, (...) but merely as an example of the so-called “out of which” cause : the material is the cause out of which an artifact is made. Next, I examine Physics II 7, a chapter in which Aristotle names "the material" as one of the four kinds of cause in its own right. But Aristotle’s model of "the material" remains the material out of which an artifact is made. (shrink)

The Platform Sutra, which dates back to the seventh century C.E., is one of the classic documents of Chinese philosophy and is the intellectual autobiography of Hui Neng, the Sixth Patriarch of Ch’an Buddhism. In the Platform Sutra, the Sixth Patriarch demonstrates that the spiritual and intellectual problems of consciousness stem from a false adherence to the dualistic standpoint. The Sixth Patriarch utilizes ingenious arguments to demonstrate how one can escape the problems of dualism. An example of a constructive engagement (...) between Chinese philosophy and Searle is to compare and contrast the arguments of Hui Neng with those of Searle. The Sixth Patriarch and Searle both reach a rather similar solution to the problem of dualism—to stop counting. In the case of the Sixth Patriarch, his solution possesses the goal of enabling the reader to achieve a spiritual liberation. Searle, in contrast, addresses the troubling epistemological problems of dualism. Searle proposes a causal monism: he claims consciousness is a state of the brain, that it is caused by processes in the brain, that it is a feature of the brain, and that it is all these at the same time. This article aims to highlight Searle’s arguments and impressive insights; it also aims to show the connection between Searle’s master insight concerning the non-duality of consciousness and the Sixth Patriarch’s realization that the difficulties of understanding consciousness stem from the formulation of the description itself. (shrink)

Avant 1812, l'actuelle République de Moldavie, partie intégrante de la région roumaine appelée Moldavie, avait comme modèle et débouché culturel la France. Après cette date, rattachée à l'Empire Russe, elle a dû rentrer, sous le nom de Bessarabie dans un tout autre giron culturel, à la frontière des civilisations. Aujourd'hui, le discours relatif à la culture et à l'identité est-il double ou dédoublé ? Certains Moldaves plaident pour leur identité roumaine, d'autres pour leur identité moldave et ceci sur un fond (...) à nombreuses touches multiculturelles. Un représentant du quartier général d'une organisation internationale a demandé à un collaborateur moldave son avis quant à la nationalité qu'il faudrait indiquer sur la liste des employés. Puisqu'au moment où, pour les ressortissants de la République de Moldavie, il a été écrit «moldave», le représentant roumain a objecté que cette nationalité n'existe pas. Si vous étiez le représentant moldave, que répondriez-vous?Before 1812, the current Republic of Moldova, then a territory of the Rumanian region called Moldova, chose France as a cultural model and outlet. After this date, the territory became part of the Russian Empire under the name of Basarabia and thus entered a completely different cultural space at the border of civilizations. Nowadays, is the discourse related to culture and identity doubled or divided? Some Moldavans opt for a Rumanian identity and others a Moldovan one in a context with many multicultural aspects. A representative of the headquarters of an international organization asked a Moldavian colleague under which nationality he should be put down on a list of employees. “Moldavian” was chosen for citizens of the Republique of Moldova only for the Rumanian representative to object that this nationality did not in fact exist. What would have been your answer to this question had you been the Moldovan representative? (shrink)

(Spanish) RESUMEN: La libertad absoluta postulada por Viktor Emil Frankl y Jean-Paul Sartre, la Shoah y la creencia en un dios omnipotente, bueno y justo parecen contradecirse. La pregunta por el sentido del sufrimiento de las víctimas del Holocausto (la verdadera catástrofe, el mayor crimen contra la humanidad), simbolizado por Auschwitz, y como punto de inflexión en la historia, es terriblemente dolorosa y parece no tener una respuesta filosófica ni teológica. A mi juicio, es importantísimo distinguir entre las víctimas inocentes (...) de la Shoah que perecieron y las víctimas inocentes que sufrieron un verdadero infierno y perdieron a sus seres queridos, pero que lograron sobrevivir. Ambas son víctimas, por supuesto, pero así como encontrarle un posible sentido al sufrimiento de las víctimas masacradas y gaseadas podría suponer un insulto a su sufrimiento y agonía –en especial, al horror que sufrieron los niños–, el horrible sufrimiento de los supervivientes pudo dar, tal vez, de alguna manera, un sentido a sus vidas después de la liberación de los campos de concentración y exterminio, ya fuera como voz, como protesta o como simple supervivencia. Frankl apuesta por un sentido último (que abraza el sentido del sufrimiento de las víctimas), y Sartre, aunque parezca no apostar por sentido alguno, volcó su vida al compromiso político después de la Segunda Guerra Mundial, y ello parece vislumbrar una minúscula pizca de sentido después de la barbarie. La filosofía de Frankl es un sí a la vida incluso en las situaciones más extremas, un grito casi nietzscheano que exalta el valor de la vida más allá de cualquier sufrimiento. Frankl, padre de la logoterapia y superviviente del Holocausto, abre una puerta a Dios al hablar de un dios inconsciente, una dimensión suprahumana y una fe incondicional, y define la religión como espiritualidad y como la búsqueda del hombre por el sentido último. Según Frankl, la libertad no se contradice con Dios, y la religión existe no a raíz de la barbarie, sino a pesar de la barbarie. El existencialismo sartreano es una filosofía de la libertad radical y de la responsabilidad. El hombre está condenado a ser libre. El ser humano es un ser en el que la existencia precede a la esencia. Somos totalmente responsables de lo que somos. Sartre afirma que la libertad humana es incompatible con Dios. En un mundo sin Dios, la moral la construyen los hombres, con sus propias decisiones y sus acciones, y la existencia y el sufrimiento de las víctimas no tienen sentido alguno. Sartre define al hombre como libertad, responsabilidad, angustia y contingencia. Frankl define al hombre como libertad, responsabilidad, espiritualidad y búsqueda de sentido. Con esta tesis me propongo entrar en la resbaladiza dimensión del dolor, la desesperación, el sentido y sinsentido del sufrimiento de las víctimas (teniendo presente los horrores de Auschwitz, que en teología y filosofía ha simbolizado desde la liberación de los campos la muerte de Dios y la muerte de la moral). Es verdad que no solo los hombres, mujeres y niños judíos fueron víctimas de la barbarie alemana, pero, como reza el mensaje de Elie Wiesel en la exposición permanente del Block 27 del Auschwitz-Birkeanu State Museum: "Not all victims were Jewish in this place, but all Jews were victims". La Shoah no es un episodio dentro de la Segunda Guerra Mundial, sino un punto de inflexión en la historia de la humanidad, y es una catástrofe que nos concierne a todos, hombres y mujeres judíos y no judíos, religiosos e irreligiosos, creyentes e increyentes, como seres libres, responsables y morales que somos –o que deberíamos ser. Muchas de las víctimas del Holocausto, en medio de la desesperación, entraron en las cámaras de gas orando, aferrándose a la esperanza de que ese final espeluznante no era un punto final. Con esta tesis no me propongo de ninguna manera responder a la eterna pregunta de si Dios existe o no, sino que propongo interpretar ese grito hacia Dios como un desesperado anhelo de esperanza. También me propongo encontrar una coherencia en las posturas de estos dos grandes pensadores para quienes la libertad y la responsabilidad definen al hombre: Frankl (quien apuesta por una dimensión suprahumana donde existe un sentido último en el que el sufrimiento de las víctimas tiene que tener algún sentido, aunque ese sentido sea completamente incomprensible en la dimensión humana) y Sartre (el existencialista ateo por excelencia, para quien el mundo, la existencia y el sufrimiento son absolutamente contingentes). En el primer capítulo expongo la logoterapia y el existencialismo sartreano: describo las tres dimensiones del hombre y las tres búsquedas de sentido propuestas por Frankl, y expongo las cinco consecuencias de "l'existence précède l'essence", centrándome en la libertad y la responsabilidad, y hablo del suicidio. El segundo capítulo está dedicado al dios inconsciente frankleano, la dimensión suprahumana, la búsqueda por el sentido último y la fe incondicional. En el tercer capítulo ilustro la libertad sin Dios sartreana, la ontología sartreana, el ateísmo sartreano y el humanismo sartreano, y hablo sobre la responsabilidad, la mauvaise foi, la contingencia, la situation y la angustia. El cuarto capítulo es necesariamente histórico (sin dejar de ser filosófico): me pregunto por la muerte de Dios después de Auschwitz, argumento y defiendo la unicidad del Holocausto (la Shoah es un punto de inflexión en la historia de la humanidad), describo las masacres antes de los campos de exterminio (Einsatzgruppen, Ordnungspolizei y Wehrmacht), el gigantesco complejo de Auschwitz (Stammlager, Auschwitz-Birkenau y Monowitz-Buna), reflexiono sobre Dios y el mal (centrándome en los niños de Auschwitz), describo los días de Frankl en Auschwitz, hablo de Dios como esperanza, de la inmortalidad y la escatología, de la crueldad de Dios, de la relación entre el cristianismo y el antisemitismo, del islam y el antisemitismo, critico el silencio de Dios, hablo de la muerte de Dios y del juicio contra Dios. En el quinto capítulo expongo la moral frankleana (una moral que atañe al hombre y no a Dios), basándome en su teoría del amor y en su única obra de teatro (Synchronisation in Binkerwald), y la moral sartreana (una moral que atañe a una humanidad sin Dios), recordando a Dostoyevsky, analizando la famosa cita de Garcin en Huis clos "L'enfer, c'est les Autres", criticando el marxismo de Sartre y cuestionando (con la mirada de Frankl y Sartre) el verso de Brecht "Erst kommt das Fressen, dann kommt die Moral"; al final del capítulo incluyo una reflexión propia y las críticas frankleana y sartreana sobre la impunidad de los verdugos y colaboradores después del Holocausto (con el permiso de Dios). Después de la Conclusión, añado un Apéndice sobre las vidas de Frankl y Sartre, para poder entender mejor su obra. PALABRAS CLAVE: logoterapia, existencialismo sartreano, búsqueda de sentido, libertad, responsabilidad, moral, angustia, sufrimiento, supervivientes, víctimas, contingencia, espiritualidad, religión, Dios, esperanza, antisemitismo, culpa, Auschwitz, Holocausto, Shoah. /// (English) ABSTRACT: The absolute freedom defended by Viktor Emil Frankl and Jean-Paul Sartre, the Shoah and the belief in an omnipotent, benevolent and just God seem to contradict each other. The question of the meaning of the victims' suffering of the Holocaust (the true catastrophe, the biggest crime against humanity), simbolised by Auschwitz and as a turning point in History, is terribly painful and doesn't seem to have an answer. In my opinion, it's crucial to distinguish between the innocent victims of the Shoah who perished and the innocent victims who sufferend a real hell and lost their loved ones, but managed to survive. Both are victims, of course, but just as finding a possible meaning to the suffering of the massacred and gassed victims could result in an insult to their suffering and agony –especially to the horror that the children suffered– the gigantic suffering of the survivors could, maybe, somehow, give a meaning to their lives after the liberation of the concentration and extermination camps, either as a voice, as a protest, or as a simple survival. Frankl believes in an ultimate meaning (that embraces the meaning of the victims' suffering), and Sartre, even if it appears not to embrace any meaning, turned his life to political engagement after War World II, and that attitude seems to give a tiny glimpse of meaning after the barbarity. Frankl's philosophy says yes to life even in the most extreme situations, and it's a Nietzschean-like scream that exalts the value of life beyond any monstrous suffering. Frankl, the father of logotherapy and a Holocaust survivor, opens a door to God when he talks about an unconscious God, a supra-human dimension and an unconditional faith; he defines religion as spirituality and as man's search for ultimate meaning. According to Frankl, freedom is not contradictory with God, and religion exists not because of the barbarity but in spite of the barbarity. Sartrean existentialism is a philosophy of radical freedom and responsibility. Men are condemned to be free. We are beings where the existence precedes the essence. We are completely responsible of what we are. Sartre argues that human freedom is incompatible with God. In a godless world, morality is constructed by people, with their own choices and actions, and human existence and the suffering of the victims don't have any meaning. Sartre defines man as freedom, responsibility, Angst and contingency. Frankl defines man as freedom, responsibility, spirituality and search for meaning. With this dissertation I attempt to enter in the slippery dimension of the pain, despair, meaning and meaninglessness of the victims' suffering (having in mind the horrors of Auschwitz, that in theology and in philosophy have simbolised, since the liberation of the camps, the death of God and the death of morality). It's true that not only Jewish men, women and children were victims of the German barbarity, but, as Elie Wiesel's message from the permanent exhibition from Block 27 of the Auschwitz-Birkeanu State Museum reads: "Not all victims were Jewish in this place, but all Jews were victims". The Shoah is not an episode inside War World II, but a turning point in the history of humankind, and a catastrophe that embraces us all, Jewish and not not Jewish men and women, religious and not religious, believers and not believers, as the free, responsible and moral beings that we all are –or that we should be. A lot of the victims, in the midst of their desperation, entered into the gas chambers praying, holding to the hope that their horrifying end was not the ultimate end. With this dissertation I do not attempt to answer the eternal question of the existence of God, rather, I will try to interpret that scream to God as a longing for hope. I also intend to find a coherence between the thought of these two great thinkers for whom freedom and responsibilty define man: Frankl (who argues that there is a suprahuman dimension where an ultimate meaning exists and where the victims' suffering has to have a meaning, even if this meaning is completely incomprehensible in the human dimension) and Sartre (the atheist existentialist par excellence, for whom the world, human existence and suffering are absolutely contingent). In the first chapter I expose logotherapy and Sartrean existentialism: I describe the three dimensions of man, the three searches for meaning, the five consequences of "l'existence précède l'essence" and I speak about suicide. The second chapter delves into the unconscious God, the supra-human dimension, the ultimate meaning and the unconditional faith. In the third chapter I expose the freedom without God defended by Sartre, Sartre's ontology, Sartre's atheism, Sartre's humanism, and his ideas about responsibility, mauvaise foi, contingency, situation, and Angst. The fourth chapter is necessarily historical (while being philosophical too): I wonder about the death of God after Auschwitz, I argue and defend the uniqueness of the Holocaust (the Shoah is a turning point in the history of humankind), I describe the massacres before the extermination camps (Einsatzgruppen, Ordnungspolizei y Wehrmacht), the gigantic Auschwitz camp complex (Stammlager, Auschwitz-Birkenau y Monowitz-Buna), I reflect on God and evil (focusing on the children of Auschwitz), I describe Frankl's days in Auschwitz, I talk about God as hope, about immortality and escathology, I discuss God's cruelty, the relationship between Christianity and antisemitism and Islam and antisemitism, I question the silence of God, and I talk about the death of God and about the trial against God. In the fifth chapter I talk about the Franklean morality (a morality that concerns man and not God), on the basis of his love theory and his only work of theater (Synchronisation in Binkerwald), and the Sartrean morality (a morality that concerns a humanity without God), remembering Dostoyevsky, analysing Garcin's famous quote in Huis clos "L'enfer, c'est les Autres", crticizing Sartre's marxism and questioning (with Frankl's and Sartre's eyes) Brecht's verse "Erst kommt das Fressen, dann kommt die Moral"; at the end of the chapter I include my own reflection (and Frankl and Sartre's critique) about the impunity of the executioners and collaborators after the Holocaust (with God's permission). After the Conclusion, I add an Appendix about the lives of Frankl and Sartre, which helps understanding better their work. KEYWORDS: logotherapy, existentialism, search for meaning, freedom, responsibility, morality, Angst, suffering, survivors, victims, contingency, spirituality, religion, God, hope, antisemitism, guilt, Auschwitz, Holocaust, Shoah. (shrink)

Cybernetics for the 21st Century Vol.1 is dedicated to the epistemological reconstruction of cybernetics, consisting of a series of historical and critical reflections on the subject – which according to Martin Heidegger marked the completion of Western metaphysics. In this anthology, historians, philosophers, sociologists and media studies scholars explore the history of cybernetics from Leibniz to artificial intelligence and machine learning, as well as the development of twentieth-century cybernetics in various geographical regions in the world, from the USA to the (...) Soviet Union, Latin America, France, Poland, China and Japan. The reconstruction shows the various paths of cybernetics and their socio-political implications, which remain unfamiliar to us today. It reveals more than what we thought we knew – and yet we hardly know – and allows us to understand where we are and to reflect on the future of technology, ecology and planetary politics. (shrink)

There has been a movement aiming to teach agents about their privilege by making the information about their privilege as costless as possible. However, some argue that in risk-sensitive frameworks, such as Lara Buchak’s (2013), it can be rational for privileged agents to shield themselves from learning about their privilege, even if the information is costless and relevant. This threatens the efficacy of these information-access efforts in alleviating the problem of elite-group ignorance. In response, I show that even within the (...) same framework, in this case David Kinney and Liam Kofi Bright’s (2021), the rationality of this information avoidance rests on shaky ground in practice. In this framework, whether an agent should avoid information depends on the precise details of (1) how relevant they expect the information to be, (2) their priors about the value of various options, and (3) their risk attitudes. The model suggests that the rationality of elite-group ignorance is a function of structural factors that are pervasive but nonetheless not insurmountable, thus offering a way out of pessimism about elite group education. (shrink)

In this paper, we report on the development of The Sustainable Port video game, which aims to simulate the complex dynamics and decisions occurring in the present and future development of a port area considering environmental aspects (CO2 emissions) and profit. To evaluate if this game fulfills its purpose, we asked 75 students and 34 employees at the Port of Rotterdam (PoR) to play The Sustainable Port. Our results show that PoR employees score higher than students suggesting a transfer between (...) real-life experience of being an employee in the port and performance in the game. Furthermore, port participants reported that The Sustainable Port can be successfully used to start discussions about the future of the Port of Rotterdam and to raise awareness about the complexity characterizing the decision-making processes occurring in a port environment. Our results, taken together, provide evidence of the effectiveness of The Sustainable Port in simulating dynamics occurring in port development and give us optimism about future applications. (shrink)

Objective: This study aimed to investigate and compare the effects of tubular gastroesophageal anastomosis and traditional gastroesophageal supra-arch anastomosis on the postoperative lung function of patients with esophageal carcinoma. -/- Methods: A total of 90 patients with middle-lower segmental esophageal cancer admitted in our hospital from August 2014 to August 2016 were recruited to our study. They were randomly divided into two groups. The observation group underwent tubular gastroesophageal anastomosis, whereas the control group underwent traditional gastroesophageal supra-arch anastomosis. Changes in (...) the postoperative pulmonary function were compared between the two groups. -/- Results: The numbers of CD4 cells (27.45 ± 5.48), CD8 cells (35.97 ± 7.16), and natural killer cells (20.79 ± 2.49), as well as the CH4/CD8 ratio (0.69 ± 0.18), of the patients in the observation group were significantly higher than the (38.45 ± 5.98), (20.45 ± 6.41), (39.44 ± 3.49), and (1.31 ± 0.48), respectively, of the patients in the control group. The differences between the two groups were statistically significant (P<0.05). By contrast, the preoperative forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), and maximum voluntary ventilation (MVV) did not significantly differ between the two groups (P>0.05). The FEV1 (1.76 ± 0.41 L), FVC (2.33 ± 0.32 L), and MVV (33.7 ± 5.2 L/min) of the observation group were significantly higher than those of the control group (P<0.05). Meanwhile, the complication rate of the observation group was 42.2%, which was significantly lower than that of the control group (75.6%) (P<0.05). -/- Conclusion: Tubular gastroesophageal anastomosis can benefit patients with esophageal cancer by significantly reducing the adverse effects on their postoperative pulmonary function and control the occurrence of postoperative complications. (shrink)

This study aimed to evaluate if eye blinks can be used to discriminate players with different performance in a session of Nintendo Entertainment System (NES) Tetris. To that end, we developed a state-of-the-art method for blink extraction from EAR measures, which is robust enough to be used with data collected by a low-grade webcam such as the ones widely available on laptop computers. Our results show a significant decrease in blink rate per minute (blinks/m) during the first minute of playing (...) Tetris. After having defined 3 groups of proficiency based on in-game performance (Novices, Intermediates, and Experts) we found out that expert players display a significantly lower decrease in blinks/m compared to novices during the first minute of gameplay, which shows that Tetris players' proficiency can be detected by looking at eye blinks/m variations during the early phase of a game session. This difference in blinks/m is observed throughout the entire game session, which supports the general conclusion that proficient Tetris players have a lower decrease in blinks/m, even when playing more difficult levels. Finally, we offer some interpretations of this effect and the relationship that our results may have with the visual cognitive workload experienced during the gameplay. (shrink)

In this study, we predict the different levels of performance in a Nintendo Entertainment System (NES) Tetris session based on the score and the number of matches played by the players. Using the first 45 seconds of gameplay, a Random Forest Classifier was trained on the five keys used in the game obtaining a ROC_AUC score of 0.80. Further analysis revealed that the number of down keys (forced drop) and the number of left keys (left translation) are the most relevant (...) keys in this task, showing that by merely including the data from these two keys our Random Forest Classifier reached a ROC_AUC score of 0.83.We conclude that the keylogger data during the early phases of a game session can be successfully used to predict performance in longer sessions of Tetris. (shrink)

The graph tong同and its associated concepts, such as da-tong (Great tong大同) and xuan-tong (mystic or dark tong玄同), have played important roles in the development of Chinese philosophy. Yet tong has received scant attention from either western or eastern scholarships. This paper is a first attempt to remedy such regret. Unlike usual understandings of tong as sameness or unity, this paper presents a nuanced account from early China, that is, ‘difference to one,’ a definition from the Mozi墨子. This definition can be (...) supported from etymological, textual, and lexical evidence. ‘Difference to one’ should not be solely attributed to a Mohist understanding; it in fact represents a common understanding of tong across philosophical streams in early China. This nuanced account provides new insights into the concept of tong in early philosophical texts, and furthermore breaks solid grounds for further studies of tong and its associated concepts. (shrink)

The Consequence Argument for incompatibilism is beset by two rival interpretations: the counterfactual sufficiency interpretation and the counterfactual might interpretation. Waldrop recently argued that the counterfactual sufficiency interpretation conflicts with certain principles governing the logic of counterfactuals. In this paper, I show that Waldrop’s argument can be adapted to prove that the counterfactual might interpretation also conflicts with the same principles. So the problem Waldrop pointed out is not peculiar to the counterfactual sufficiency interpretation.

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

Xuantong 玄同 (tentatively translated as dark oneness) is a unique Daoist idea that represents an ideally mental and physical state as a result of cultivation. However, owing to limited context in the Laozi, there is no consensus on the interpretation of xuantong. Contemporary studies have also neglected xuantong’s evolution in early texts and assumed a homogeneous understanding, and hence, failed to provide a nuanced account. In this article, I investigate how xuantong evolves from the Guodian Laozi to the Huainanzi and (...) Wenzi. I argue that although xuantong may originate from the Laozi, it is in the Wenzi that a coherent theory of xuantong is accomplished. This theory advocates an orderly process of cultivation that covers internal mental states, external acts, and integration with the whole universe. The cultivation would eventually lead people to adopt an undifferentiated perspective on, and reach oneness with, all things in the universe. (shrink)

To obtain effective fusion results of multi source evidences with different importance, an evidence fusion method with importance discounting factors based on neutrosopic probability analysis in DSmT framework is proposed. First, the reasonable evidence sources are selected out based on the statistical analysis of the pignistic probability functions of single focal elements. Secondly, the neutrosophic probability analysis is conducted based on the similarities of the pignistic probability functions from the prior evidence knowledge of the reasonable evidence sources. Thirdly, the importance (...) discounting factors of the reasonable evidence sources are obtained based on the neutrosophic probability analysis and the reliability discounting factors of the real-time evidences are calculated based on probabilistic-based distances. Fourthly, the real-time evidences are discounted by the importance discounting factors and then the evidences with the mass assignments of neutrosophic empty sets are discounted by the reliability discounting factors. Finally, DSmT+PCR5 of importance discounted evidences is applied. Experimental examples show that the decision results based on the proposed fusion method are different from the results based on the existed fusion methods. Simulation experiments of recognition fusion are performed and the superiority of proposed method is testified well by the simulation results. (shrink)

The standard Lewis–Stalnaker semantics of counterfactuals, given the Strong Centering Thesis, implies that all true–true counterfactuals are trivially true. McGlynn developed a theory, based on Penczek, to rehabilitate the non-triviality of true–true counterfactuals. I show here that counterfactuals with true but irrelevant components are counterexamples to McGlynn’s account. I argue that an extended version of the connection hypothesis is sustainable, and grounds a full theory of counterfactuals explicable in a broadly standard way, if an indispensable asymmetry between semifacuals and other (...) counterfactuals is acknowledged. (shrink)

The ‘Wu xing’ belongs to Guodian bamboo slips texts, which were buried around 300 BCE and excavated in 1993. Its relation with Mengzi is widely investigated. Yet how it is philosophically related to Xunzi receives little attention. In this article, I illustrate a neglected relation between ‘Wu xing’ and Xunzi, by elucidating how shan 善 (goodness) is first raised in ‘Wu xing’ and developed by Xunzi into a concrete idea. Both ‘Wu xing’ and Xunzi propose that shan exists in action, (...) which boils down to the harmonious unity of the mind and body, and to secure the ideal relation between the mind and body requires constant learning and practicing, particularly, of rituals. Learning and practicing not only lead one to realize shan, but eventually to become a consummate practitioner of rituals, to use Xunzi’s words, to become a sage. (shrink)

A well-documented “beauty is good” stereotype is expressed in the expectation that physically attractive people have more positive characteristics. Recent evidence has also found that unattractive faces are associated with negative character inferences. Is what is good (bad) also beautiful (ugly)? Whether this conflation of aesthetic and moral values is bidirectional is not known. This study tested the hypothesis that complementary “good is beautiful” and “bad is ugly” stereotypes bias aesthetic judgments. Using highly controlled face stimuli, this preregistered study examined (...) whether moral character influences perceptions of attractiveness for different ages and sexes of faces. Compared to faces paired with nonmoral vignettes, those paired with prosocial vignettes were rated significantly more attractive, confident, and friendlier. The opposite pattern characterized faces paired with antisocial vignettes. A significant interaction between vignette type and the age of the face was detected for attractiveness. Moral transgressions affected attractiveness more negatively for younger than older faces. Sex-related differences were not detected. These results suggest information about moral character affects our judgments about facial attractiveness. Better (worse) people are considered more (less) attractive. These findings suggest that beliefs about moral goodness and physical beauty influence each other bidirectionally. (shrink)

How does aging affect facial attractiveness? We tested the hypothesis that people find older faces less attractive than younger faces, and furthermore, that these aging effects are modulated by the age and sex of the perceiver and by the specific kind of attractiveness judgment being made. Using empirical and computational network science methods, we confirmed that with increasing age, faces are perceived as less attractive. This effect was less pronounced in judgments made by older than younger and middle-aged perceivers, and (...) more pronounced by men (especially for female faces) than women. Attractive older faces were perceived as elegant more than beautiful or gorgeous. Furthermore, network analyses revealed that older faces were more similar in attractiveness and were segregated from younger faces. These results indicate that perceivers tend to process older faces categorically when making attractiveness judgments. Attractiveness is not a monolithic construct. It varies by age, sex, and the dimensions of attractiveness being judged. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

The Philosophical Forum, Volume 53, Issue 1, Page 47-61, Spring 2022.

This article investigates a central yet perplexing term yiming in the ‘Qiwulun’ chapter of the Zhuangzi. Yiming describes a crucial way to detach from epistemic distinctions and debates. This term is often explained as ‘using ming’ or contradictorily as ‘stopping ming’. Yet neither of the two explanations can provide a full understanding of how yiming is adopted. I take three steps to explain yiming. First, taking an etymological approach, I argue that ming can be formulated as ‘X shining on Y’. (...) Second, I use the formula of ‘X shining on Y’ to account for yiming and argue that this term refers specifically to ‘using tian to shine on everything’. Third, I unpack a cluster of tian-associated metaphors, which provides a deep understanding of yiming as an ideal way to mental tranquility. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Hegel definiert „Vernunft” als die Einheit der Objektivität und der Subjektivität. Diese Definition bedeutet nicht, dass für Hegel nur das Subjekt existiert, welches sich das Objekt dementsprechend nur in seinem Inneren vorstellt; eine solche Definition bedeutet nämlich nicht, dass es für Hegel keine Außenwelt gibt, sondern eigentlich, dass es für ihn nichts gibt, was als solches unvernünftig ist. Als Einheit des Subjekts, das erkennt, und des Objekts, das erkannt wird, umfasst die Vernunft für Hegel alles, was es gibt und geben (...) kann. Jene Definition bedeutet eben: Es gibt nichts außerhalb dessen, was das Subjekt erkennt und erkennen kann. Mit dieser These verneint Hegel selbstverständlich nicht, dass es Sachen gibt, die das Subjekt noch nicht kennt bzw. von deren Existenz es noch nicht weiß, und auch nicht, dass es keine Sachen gibt, die das Subjekt noch nicht verstanden und begriffen hat, sondern eigentlich nur, dass es keine Sachen gibt, die prinzipiell nicht erkannt und begriffen werden können. Dass etwas existiert, impliziert für Hegel, dass es eventuell erkannt und fernerhin begriffen werden kann. Sein, Erkennbarsein und Begreifbarsein sind für Hegel ein und dasselbe. (shrink)

Aim: Low professional help-seeking intention (PHSI) hinders effective treatment of mental illness. PHSI among Chinese students is still understudied and under-recognized. This study aimed to evaluate the status of PHSI and its associated risk factors among Chinese medical students. -/- Methods: A cross-sectional survey was conducted in Hainan province, South China, between January 1, 2021, and May 31, 2021. A total of 2182 medical students were recruited and surveyed via an anonymous structured questionnaire. Logistic regression analyses were performed to identify (...) the factors associated with PHSI. -/- Results: Among the 2182 medical students (mean age 21.0 years (SD = 3.70), 61.5% females), those with and without PHSI were 72.0% and 28.0%, and 16.4% with moderate to severe depression. Male students, those with a high level of depression stigma, serious family dysfunction, and heavy dependence on mobile phones were significantly less likely to seek professional mental health help, with odds ratios (ORs) of 1.5, 2.0, 2.1, and 1.7, respectively. -/- Conclusion: A significant proportion of Chinese medical students demonstrate low PHSI, influenced by factors such as gender, depression stigma, family dysfunction, and mobile phone dependence. Future interventions aimed at increasing medical students’ PHSI should prioritize reducing depression stigma, mitigating reliance on mobile phone use, and enhancing family function to address these key barriers to seeking professional mental health support. (shrink)

The concept of tong played an important role in early Chinese political thought, as in the “Shangtong” chapter of the Mozi and the “Liyun” chapter of the Liji. Nevertheless, tong as a political thought has received little scholarly attention. In this article, I diverge from the common understandings of tong as sameness or unity and call on etymological and textual evidence to suggest that tong fundamentally refers to “difference to one.” In light of this understanding of tong as “difference to (...) one,” I focus on the “Shangtong” and the “Liyun” and compare the two visions of political tong that the two chapters present. With this research, I argue that the “Shangtong” and “Liyun” represent two different political streams as to how to unite a society with early China’s differences and divisions. (shrink)

ABSTRACT:Drawing upon John Rawls's framework inThe Law of Peoples,this paper argues that MNEs have a responsibility to promote well-ordered social and political institutions in host countries that lack them. This responsibility is grounded in a negative duty not to cause harm. In addition to addressing the objection that promoting well-ordered institutions represents unjustified interference by MNEs, the paper provides guidance for managers of MNEs operating in host countries that lack just institutions. The paper argues for understanding corporate responsibility in relation (...) to the specific institutional environment in which MNEs operate. (shrink)

In this study, we analyzed the blinking behavior of players in a video game tournament. Our aim was to test whether spontaneous blink patterns differ across levels of expertise. We used blink rate, blink duration, blink frequency, and eyelid movements represented by the Eye Aspect Ratio (EAR) to train a machine learning classifier to discriminate between different levels of expertise. Classifier performance was highly influenced by features such as the mean, standard deviation and median EAR. Moreover, further analysis suggests that (...) blinking rate and blink duration are likely to increase along with the level of expertise. We speculate this may be indicative of a reduction in cognitive load and lowered stress of expert players. In general, our results suggest that EAR and blink patterns can be used to identify different levels of expertise of video game players. (shrink)

In post-Gricean pragmatics, communication is said to be successful when a hearer recovers a speaker’s intended message. On this assumption, proposals for ‘what is said’ – the semantic, propositional meaning of a speaker’s utterance – are typically centred around the content the speaker aimed to communicate. However, these proposals tend not to account for the fact that speakers can be deliberately vague, leaving no clear proposition to be recovered, or that a speaker can accept a hearer’s misconstrual even though the (...) speaker didn’t intend it. In such cases, identifying ‘what is said’ is more contentious, even though communication is arguably no less successful. Building on recent interactionist approaches to meaning, this chapter offers a proposal for ‘what is said’ that can account for cases of ‘imperfect’ communication in which the recovery of a speaker’s intention goes awry. This involves taking ‘what is said’ as the co-constructed meaning that the speaker and hearer jointly agree on, giving ‘grounded meanings’ – those mutually and manifestly accepted into the discourse by speaker and hearer – higher precedence in a theory of communication than simply the speaker’s intended meaning. In such cases, rather than speaker and hearer converging at the level of explicit utterance content, communication is expected to be successful as long as the hearer recovers a proposition which is compatible with the speaker’s higher-order discursive goal. The hearer’s uptake is then allowed to override the content of the speaker’s intended meaning in the process of negotiating ‘what is said’. (shrink)

Considerable evidence proves that causal learning and causal understanding greatly enhance our ability to manipulate the physical world and are major factors that distinguish humans from other primates. How do we enable unintelligent robots to think causally, answer the questions raised with "why" and even understand the meaning of such questions? The solution is one of the keys to realizing artificial intelligence. Judea Pearl believes that to achieve human-like intelligence, researchers must start by imitating the intelligence of children, so he (...) proposed a "causal inference engine" to help future artificial intelligence make causal inference, pass the Minimal Turing Test, and even become a moral subject who can discern good from evil. This study attempts to provide some insights into the development of children's education from basic assumptions and construction goals of artificial intelligence, and to reflect on the causal model of artificial intelligence through children's education. (shrink)

This paper aims to bridge the relationship between metalinguistic if you like as a non-propositional discourse marker and its conditional counterparts. This paper claims that metalinguistic if you like is polysemous between a hedge that denotes the speaker’s reduced commitment to some aspect of the main clause, and an optional yet potential conditional reading that interlocutors can legitimately draw on in interaction which is brought about due to the ‘if p, q’ sentence form. That is, although the metalinguistic reading is (...) most likely obtained automatically by default, it also carries an available conditional reading that is akin to other metalinguistic conditional clauses such as if you see what I mean. Next, a semantic representation of metalinguistic if you like is developed that takes on board a characterization of conditionality that departs from lexico-grammatical conventions, such that conditionals of the form ‘if p, q’ no longer bear a one-to-one correspondence with “conditional” truth conditions. Employing a radical contextualist semantic framework in which the unit of truth-conditional analysis is not constrained to the sentence form, utterances employing metalinguistic if you like are given a semantic representation such that the if-clause does not contribute propositional content, yet they also maintain their status as conditionals as the sentence form gives rise to a potential conditional secondary meaning. (shrink)

Low-carbon agriculture is essential for protecting the global climate and sustainable agricultural economics. Since China is a predominantly agricultural country, the adoption of low-carbon agricultural technologies by local farmers is crucial. The past literature on low-carbon technologies has highlighted the influence of demographic, economic, and environmental factors, while the psychological factors have been underexplored. A questionnaire-based approach was used to assess the psychological process underlying the adoption of low-carbon agricultural technologies by 1,114 Chinese rice farmers in this paper, and structural (...) equation modeling (SEM) was empirically employed to test our theoretical model. (shrink)

Abstract: Women under-representation in senior management post inside academic organizations remains to be an issue which needs a serious concern at national and international levels. Thus, women leaders are not in place to champion the change process. Societies, organizations and people themselves have determined that, only the males make good leaders. The gender status in the senior management positions in HE in Tanzania is virtually non-existent. Data was sourced through administered questionnaire, FGD and interview where’s senior academic and non-academic staff, (...) together with senior university management officials were involved. Results in all seven studied universities that is SUA, MU, UDSM, JUCO, MuM and UDOM, show the positions of VC, DVCA and DVCAF to be headed by men except OUT which has a female DVCAA. Basing on the findings of this study, the researcher recommended on the transparency of procedures for recruitment and promotion, empowering women to meet employment criteria, developing a gender management system as well as mentoring and establishment of the networks for women in order to close the prevailing gender leadership gap. (shrink)

Abstract: This article mainly intends to identify barriers that cause the under-representation of women in top leadership positions in higher education in Tanzania. The study comprises the sample of 250 respondents with the use of a case study research design constructed on the application of mixed methods (qualitative and quantitative). Thus, non-probability sampling was applied to qualitative data collection while probability sampling was used in quantitative data. The findings show the fundamental relationship between individual, administrative and societal factors that block (...) women to reach the top leadership position in universities. Besides, the study has demonstrated the gender mainstreaming as the system which can be connected to adjust the hierarchical structures, methods and culture and bring the positive condition which advance gender equality. Nevertheless, as the well-known saying "Fix the holes in the pipe" goes, the variety of actions and activities are needed. Thus, in accordance with the proof from the study and individual encounters, the researcher, marked on Focused Gender Research, Capacity Development Programs, Parliamentary Charter, Setting Targets as well as Regular Monitoring and Reporting as interventions sustainable for bridging the prevailing gender leadership gap in higher education in Tanzania. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Ambient assisted living technologies are increasingly presented and sold as essential smart additions to daily life and home environments that will radically transform the healthcare and wellness markets of the future. An ethical approach and a thorough understanding of all ethics in surveillance/monitoring architectures are therefore pressing. AAL poses many ethical challenges raising questions that will affect immediate acceptance and long-term usage. Furthermore, ethical issues emerge from social inequalities and their potential exacerbation by AAL, accentuating the existing access gap between (...) high-income countries and low and middle-income countries. Legal aspects mainly refer to the adherence to existing legal frameworks and cover issues related to product safety, data protection, cybersecurity, intellectual property, and access to data by public, private, and government bodies. Successful privacy-friendly AAL applications are needed, as the pressure to bring Internet of Things devices and ones equipped with artificial intelligence quickly to market cannot overlook the fact that the environments in which AAL will operate are mostly private. The social issues focus on the impact of AAL technologies before and after their adoption. Future AAL technologies need to consider all aspects of equality such as gender, race, age and social disadvantages and avoid increasing loneliness and isolation among, e.g. older and frail people. Finally, the current power asymmetries between the target and general populations should not be underestimated nor should the discrepant needs and motivations of the target group and those developing and deploying AAL systems. Whilst AAL technologies provide promising solutions for the health and social care challenges, they are not exempt from ethical, legal and social issues. A set of ELSI guidelines is needed to integrate these factors at the research and development stage. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

In this position paper, we have used Alan Cooper’s persona technique to illustrate the utility of audio- and video-based AAL technologies. Therefore, two primary examples of potential audio- and video-based AAL users, Anna and Irakli, serve as reference points for describing salient ethical, legal and social challenges related to use of AAL. These challenges are presented on three levels: individual, societal, and regulatory. For each challenge, a set of policy recommendations is suggested.

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

In Recursivity and Contingency, Yuk Hui prompts a rigorous historical and philosophical analysis of today’s algorithmic culture. As evidenced by highspeed AI trading, predictive processing algorithms, elastic graph-bunching biometrics, Hebbian machine learning and thermographic drone warfare, we are privy to an epochal technological transition. As these technologies, stilted on inductive learning, demonstrate, we no longer occupy the moment of the ‘storage-and-retrieval’ static database but are increasingly engaged with technologies that are involved in the ‘manipulable arrangement’ (p204) of the indeterminable. It (...) is, in fact, extricating the indeterminable or the Inhuman and its cosmic anti-capitalist imperative that concerns the core of Hui’s project of technodiversity. (shrink)