Diss.--München, 2003. / Bibliogr. p. 353-359.

It is widely known that we can expect great damage to our world and economy because of climate change. It is human activities, and their emissions that has led us to where we are. IEA (2022) have declared that coal is the single largest source of carbon emission and scientists have stated that we need to phase-out the use of coal by 2050 to reach the Paris Agreement goal. At COP26 India chose to rephrase the climate agreement from “phase out the use of coal” to “phase down the use of coal” even though this goes against the recommendations made by scientists. This paper models the damage to GDP from climate change using a DGE model with two regions. One region is represented by India and the other is represented by the rest of the world. To predict the economic damages from using coal the model includes a climate variable. The thesis investigates four different scenarios: both regions collaborate; India defects while the rest of the world collaborates; the rest of the world defects while India collaborates; both regions defect. The results show that in 100 years the temperature will have risen to 3.27 degrees if the two regions choose to defect and the damage to GDP will be 1.55 percent. This is 0.21 degrees and 0.14 percentage points higher than when both regions collaborate. By using a game theory set-up, I find that it is always beneficial for India to defect. While for the rest of the world, it is better to collaborate in the long run to minimize their damages.

L'huître creuse C. gigas a connu des épisodes récurrents de mortalités estivales. En 2009, l'ostréiculture a connu la plus grave crise écologique et économique jamais observée depuis l'introduction de cette espèce sur les côtes françaises. Les études réalisées précédemment dans le but de comprendre les causes de ces mortalités, attribuent une origine multifactorielle faisant intervenir, de manière concomitante, des paramètres environnementaux, des conditions physiologiques particulières de l'huître, en association à la présence de microorganismes pathogènes tels que les vibrions appartenant aux espèces V. aestuarianus, V. splendidus et le virus OsHV-1. Ainsi, l'ensemble des travaux menés au cours de cette thèse représentent une contribution à l'étude d'une réponse immunitaire efficace de l'huître creuse Crassostrea gigas aux infections vibrions pathogènes.Le travail de thèse qui vous a été présenté a été réalisé dans le but de progresser encore sur la compréhension de la réponse immunitaire de l'huître creuse. Ce travail nous a permis d'établir une cartographie des modifications transcriptionnelles par la technique DGE (Digital Gene Expression) et notamment par l'identification d'effecteurs ou mécanismes entrant en jeu dans une réponse efficace vis-à-vis des agents infectieux et conduisant à son élimination. Le modèle (Crassostrea gigas – V. aestuarianus/V. splendidus) s'est avéré adapté à cette étude. Les mécanismes identifiés au cours de cette thèse, devront être étudiés plus précisément, puisque la plupart des gènes surreprésentés chez les huîtres survivantes ont des fonctions putatives. Nous avons suggéré l'implication de ces gènes dans le processus de survie des huîtres au cours d'une réponse efficace aux infections bactériennes. Il est apparu nécessaire de développer des recherches autour des défenses de l'huître creuse C. gigas avec pour objectif le développement de stratégies destinées à limiter l'impact des maladies. A long terme, ces stratégies seront applicables soit en prophylaxie afin de détecter des déficiences et prévenir le développement de maladies, soit en sélection génétique pour le criblage de géniteurs présentant des capacités de défenses optimales. / Aquatic organisms and particularly marine invertebrates, such as the oyster Crassostrea gigas, harbour an abundant and diverse microflora on their surface (epibiosis) or inside their tissues (endobiosis) where Vibrio splendidus is found as a dominant culturable Vibrio. With Evolution, oysters have developed effective systems for maintaining their homeostasis and discriminating the bacteria beneficial for their physiological fitness from the potentially harmful and pathogenic ones. However, for decades, the cultivated Pacific oyster C. gigas is suffering large scale summer mortality phenomenon that is reported in all areas of the world where this species is cultivated. Considerable effort has been invested in advanced genomic technologies to understand and characterize the major traits that govern the tolerance of oysters to stressful culture conditions and to pathogenic bacteria. In particular, immune-related genes have been characterized from C. giga. Briefly, a variety of antimicrobials have been fully characterized. Whereas most of these immune genes were shown to be modulated during infections, the molecular mechanisms by which the oyster can survive virulent Vibrio infections remained totally unknown. Here, our objective was to develop a better understanding of the genetic-level responses of oysters to pathogenic versus non pathogenic bacteria and to identify genes that are involved in physiological and immune responsiveness to circumvent the infections. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster immunity (hemocytes), using Digital Gene Expression (DGE). The study aimed to compare the expression profiles of the two libraries and, beyond gene identification and functional annotation, to explore the putative functions involved in the capability of oysters to circumvent and to survive infections. This is the first report on genome-wide transcriptional analysis of oyster survival-responsiveness.

Inaug.-Diss.--Bonn, 1967. / Includes bibliographical references (p. 438-463).

Vysoce výkonné sekvenční technologie produkují obrovské množství dat, která mohou odhalit nové geny, identifikovat splice varianty a kvantifikovat genovou expresi v celém genomu. Objem a složitost dat z RNA-seq experimentů vyžadují škálovatelné metody matematické analýzy založené na robustníchstatistických modelech. Je náročné navrhnout integrované pracovní postupy, které zahrnují různé postupy analýzy. Konkrétně jsou to srovnávací testy transkriptů, které jsou komplikovány několika zdroji variability měření a představují řadu statistických problémů. V tomto výzkumu byla sestavena integrovaná transkripční profilová pipeline k produkci nových reprodukovatelných kódů pro získání biologicky interpretovovatelných výsledků. Počínaje anotací údajů RNA-seq a hodnocení kvality je navržen soubor kódů, který slouží pro vizualizaci hodnocení kvality, potřebné pro zajištění RNA-Seq experimentu s analýzou dat. Dále je provedena komplexní diferenciální analýza genových expresí, která poskytuje popisné metody pro testované RNA-Seq data. Pro implementaci analýzy alternativního sestřihu a diferenciálních exonů jsme zlepšili výkon DEXSeq definováním otevřeného čtecího rámce exonového regionu, který se používá alternativně. Dále je popsána nová metodologie pro analýzu diferenciálně exprimované dlouhé nekódující RNA nalezením funkční korelace této RNA se sousedícími diferenciálně exprimovanými geny kódujícími proteiny. Takto je získán jasnější pohled na regulační mechanismus a poskytnuta hypotéza o úloze dlouhé nekódující RNA v regulaci genové exprese.

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This dissertation explores the innovation and creativity behind elite Gelukpa thinking and writing about Buddhist place in Tibet in the long eighteenth century. It argues that writing about place offered Geluk thinkers a way to embed themselves in the land and history of Tibet, giving a rooted support to their expanding influence. More broadly, it demonstrates a growing spatialization of religious thought in Tibet and reveals a continuous and dynamic conversation around Tibetan Buddhist place and the nature of Buddhist space. This conversation went to the heart of matters of history, power, religion, and aesthetics and was tied intimately to the historical context of its production. To contextualize the period of Gelukpa growth, I begin by presenting the history of Tibetan Buddhist place writing across the longue durée. Based on my collection and analysis of over 400 place writing texts, including guidebooks, histories, poetry, and ritual texts, I suggest for the first time a periodization for this history, delineating distinct phases in the development of place writing across time. This periodization reveals that at most points throughout this history, Nyingma writers dominated place writing production. From the twelfth to seventeenth centuries, they set the standard for traditional place writing genres like guidebook literature. Beginning at the end of the seventeenth century, however, Gelukpa authors joined the conversation with great energy, producing both traditional and new styles of place writing in greater numbers than ever seen before. Why did the long eighteenth century see a burgeoning of place writing, both generally and by Gelukpa authors, specifically, and what characterized these new texts? I explore these questions by looking more closely at the work of three Gelukpa writers. First, I show how place writing was part of the Gelukpa rise to political and institutional dominance by an analysis of the Fifth Dalai Lama’s use of the supine demoness narrative in his efforts to unify Tibet under his government. Gelukpa place writing of this period was forced to grapple with earlier Nyingma narratives that in many cases dominated the conversation. Sumpa Khenpo’s Annals of Blue Lake offers an example of the creativity with which writers presented their new visions for Buddhist place in Tibet. Finally, I look at the poetry of Tukwan Lozang Chökyi Nyima as evidenced of the incorporation of new spatial configurations and the cultural exchange happening due to increased interactions with the Qing capital and imperial patronage. These snapshots ultimately show that the Gelukpa used place writing as part of its efforts to cement a growing influence politically, geographically, and culturally in Tibet and across Asia in the long eighteenth century. Just as importantly, however, these examples exhibit the creative power of writers in shaping the Buddhist landscape of Tibet. Through an analysis of an array of place writing texts, this dissertation brings to light one moment in the long history of Tibetan Buddhist place writing and demonstrates that Buddhist place has been a site of dynamic conversation (and often contestation) throughout that history.

準噶爾在噶爾丹的統治下逐漸成為中亞的強國，隨著勢力的增強準噶爾企 圖統一蒙古各部。準噶爾興起的時間恰巧與清朝興起的時間相同，清朝當 時已統一了漠南蒙古，中原地區的反抗勢力也漸漸消弭了，逐步加強國內 的統治。清朝一向視喀爾喀、漠南蒙古為屏障之地，正與準噶爾統一蒙古 各部的計劃相衡突，因而引發清朝與準噶爾近七十年（1690年- 1758年） 的抗衡。本篇論文即是研究從準噶爾汗噶爾丹時期到恰克圖驗阿睦爾撒納 屍首為止，其間準噶爾與清朝的關係。著重點是在分析準噶爾與清朝在爭 奪領土與黃教控制權上，雙方勢力的消長，進而研究清朝初期的邊疆政策 。本篇論文除緒論、結論外，分為四章：第一章在討論康熙、雍正年間， 清廷對準噶爾的經略，企圖與俄國、土爾扈特聯合夾擊準噶爾。第二章， 討論準噶爾與清朝間的開市貿易，清廷對開市貿易的態度。第三章，討論 準噶爾與清朝爭奪西藏黃教控權的問題，看清廷對黃教的控制。第四章， 則在討論朝隆年間，清廷對準噶爾的用兵，重新審視阿睦爾撒納的叛清行 動。

本篇論文主要是以藏傳佛教的格魯派所詮釋的中觀應成派思想，來反思Axel Honneth批判理論。雖然兩者都共同關懷如何解決現實的痛苦，都努力提出一個能夠具體解決當前人類不滿的實踐方案，但由於兩者所辨認的痛苦成因有所差異，因此提出了不同的解決之道。本篇論文站在中觀應成派「二諦」的角度，認為Honneth所提出的批判理論並沒有正確地辨認出痛苦的根源「自性執」，而僅僅提出了「世俗諦」層次的解決方案，因而無法真正地對症下藥，從根源之處解決痛苦。 本篇論文企圖論證以下兩個命題：第一，我們必須正確地掌握「作為痛苦的根源的自性執」，如果不透過這個步驟，就沒有辦法根本地解決痛苦。進一步我們應該要了解到，Honneth批判理論本身也是自性空的，否則一個企圖解決痛苦的理論資源，本身反而就是增加痛苦根源的一部份。第二，由於「黑格爾左翼的批判理論」所提倡的「具體地提出具有交互主體性的解決痛苦的實踐方案」這個訴求是作為中觀應成派與批判理論的共同關懷，因此，我也企圖說明從「二諦」的觀點出發，並不會與這個基本關懷相衝突，如此一來，就能夠說明以中觀應成派的二諦作為分析基礎，是具有社會實踐的潛力的。 為了論證這兩個命題，本文的章節安排如下。首先，第一章作為導論，說明全篇文章的論證架構。第二章則說明Honneth所定位的批判理論，即「黑格爾左翼」及其重要的概念「內在超越」的意涵。這樣的方法論特別強調了「對當前的痛苦提出具體的實踐性解決方案」的訴求。在第三章中，我把焦點放在Honneth所提出的「為承認而鬥爭」的批判理論模型，主要的目的是概要出承認理論的根本命題。在第四章中，我會討論中觀應成派的幾個主要概念，即「所破」和「二諦」，希望透過這三個概念能夠概要出格魯派思想的核心，並以此為基礎來形成反省Honneth批判理論的基礎架構。第五章則具體地說明「Honneth承認理論各個概念的空性」。我將從中觀應成派的思想中，提取較為相關的討論來進行說明，包括了「『人』無自性」、「『行動與行動者』無自性」、「『貪欲與貪者』無自性」以及「『苦』無自性」等等討論，這些都是對應於Honneth承認理論的核心概念而來。第六章為結論，以前五章的討論為基礎，重新說明上述的兩個命題。 / In this thesis, I want to reflect Axel Honneth's critical theory through Tibetan Buddhism dGe Lugs pa, founded by Tsongkhapa in the fourteen century, who followed and expounded the thought of prAsaGgika-mAdhyamika. Both Honneth and dGe Lugs pa are focusing how to comfort people's suffering realistically and practically. However, by means of the thought of dGe Lugs pa, especially the view of two-truths, we could point out that Honneth's approach would fail to solve the problem causing people's suffering completely, because he did not recognize the real cause of the suffering. In the view of dGe Lugs pa, our suffering is resulted from the innate ignorance in our consciousness which grasps everything as existing truly and inherently. I want to prove two propositions in this thesis: in the first place, I argue that we can't really comfort our suffering completely unless we recognize the true cause of the suffering, the ignorance of seeing things inherently existing, and transform it rightly by means of understand that everything is empty of inherent existence without exception. I will reflect Honneth's critical theory and find that all essential concepts of his theory of recognition are empty of inherent existence. Secondly, I argue that if we rightly understand dGe Lugs pa's thought, we would not abandon the goal of practically resolving the problems causing people's suffering, which is the common interest of Axel Honneth and dGe Lugs pa. In order to prove these two propositions, I arrange the thesis into six chapters. The first chapter is the introduction to the thesis's main arguments. The following two chapters focus on Honneth's critical theory: in chapter two I will illustrate the so called " left-Hegelianism", by this concept Honneth emphasis the critical theory which is directed to diagnosis the social pathology, and accordingly transform it practically through social praxis; the third chapter will elaborate the model of "struggle for recognition", which is founded by Honneth to revive the left-Hegelianism critical theory at the present time. In chapter four I will illustrate some essential concepts of dGe Lugs pa, including the concept of svabhAva, two-truths and bodhicitta. Through these illustrations I want to found the tool for pointing out the misrecognition of the cause of suffering in Honneth's critical theory, and explain the dGe Lugs pa's alternative solution to the problem causing people's suffering. In fifth chapter, some reasoning using for proving the emptiness of inherent existence will be expounded, the concepts which we want to show empty of inherent existence are: "I", persons, actor, act, suffering, the person who suffers, desirous one and the desire. These concepts are those essential for Honneth's critical theory. By means of understanding the emptiness of these concepts, we will understand those concepts Honneth used for constructing his theory are empty of inherent existence. In chapter six, the conclusion of this thesis, I will use the resources illustrated in above five chapters to restate the two propositions arguing in the introduction.

<p dir="ltr">The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects but does not necessarily indicate the initial point of interference within a network. The objective of this project is to take advantage of large scale and genome-wide perturbational or Perturb-Seq datasets by using them to pre-train a generalist machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of single cell RNA sequencing data collected from CRISPR knock out screens in cell culture. The advent of generative machine learning algorithms, particularly transformers, make it an ideal time to re-assess large scale data libraries in order to grasp cell and even organism-wide genomic expression motifs. By tailoring an algorithm to learn the downstream effects of the genetic perturbations, we present a pre-trained generalist model capable of predicting the effects of multiple perturbations in combination, locating points of origin for perturbation in new datasets, predicting the effects of known perturbations in new datasets, and annotation of large-scale network motifs. We demonstrate the utility of this model by identifying key perturbational signatures in RNA sequencing data from spaceflown biological samples from the NASA Open Science Data Repository.</p>