Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross

Somers, Daryl,Gyenis, L.,Yun, S.J.,Smith, K.P.,Steffenson, B.J.,Bossolini, E.,Sanguineti, M.C.,Muehlbauer, G.J. National Research Council of Canada, Conseil natio 2007 Genome Vol.50 No.8

<P> Hordeum vulgare subsp. spontaneum is the progenitor of cultivated barley (Hordeum vulgare L.). Domestication combined with plant breeding has led to the morphological and agronomic characteristics of modern barley cultivars. The objective of this study was to map the genetic factors that morphologically and agronomically differentiate wild barley from modern barley cultivars. To address this objective, we identified quantitative trait loci (QTLs) associated with plant height, flag leaf width, spike length, spike width, glume length in relation to seed length, awn length, fragility of ear rachis, endosperm width and groove depth, heading date, flag leaf length, number of tillers per plant, and kernel color in a Harrington/OUH602 advanced backcross (BC2F8) population. This population was genotyped with 113 simple sequence repeat markers. Thirty QTLs were identified, of which 16 were newly identified in this study. One to 4 QTLs were identified for each of the traits except glume length, for which no QTL was detected. The portion of phenotypic variation accounted for by individual QTLs ranged from about 9% to 54%. For traits with more than one QTL, the phenotypic variation explained ranged from 25% to 71%. Taken together, our results reveal the genetic architecture of morphological and agronomic traits that differentiate wild from cultivated barley. </P>

CAPS markers specific to E^b, E^e, and R genomes in the tribe Triticeae

Somers, D.J.,Li, X.-M.,Lee, B.S.,Mammadov, A.C.,Koo, B.-C.,Mott, I.W.,Wang, R.R.-C. Canadian Science Publishing 2007 Genome Vol.50 No.4

<P> Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Understanding their genome compositions is pivotal for efficient use of this vast gene pool in germplasm-enhancement programs. Several cleaved amplified polymorphic sequence (CAPS) markers were developed to distinguish the E<SUP>b</SUP>, E<SUP>e</SUP>, and R genomes. With the aid of disomic addition lines of wheat, it was confirmed that all 7 chromosomes of E<SUP>b</SUP>, E<SUP>e</SUP>, and R genomes carry these genome-specific CAPS markers. Thus, the identified CAPS markers are useful in detecting and monitoring the chromosomes of these 3 genomes. This study also provides evidence suggesting that some Purdue and Chinese germplasm lines developed for barley yellow dwarf virus (BYDV) resistance are different from those developed in Australia. Furthermore, Thinopyrum intermedium and Thinopyrum ponticum were shown to have different genome constitutions. Sequence analyses of the 1272 bp sequences, containing Ty3/gypsy retrotransposons, from the E<SUP>b</SUP>, E<SUP>e</SUP>, and R genomes also shed light on the evolution of these 3 genomes. </P>

Cystoscopic depth estimation using gated adversarial domain adaptation

Peter Somers,Simon Holdenried-Krafft,Johannes Zahn,Johannes Schüle,Carina Veil,Niklas Harland,Simon Walz,Arnulf Stenzl,Oliver Sawodny,Cristina Tarín,Hendrik P. A. Lensch 대한의용생체공학회 2023 Biomedical Engineering Letters (BMEL) Vol.13 No.2

Monocular depth estimation from camera images is very important for surrounding scene evaluation in many technical fieldsfrom automotive to medicine. However, traditional triangulation methods using stereo cameras or multiple views with theassumption of a rigid environment are not applicable for endoscopic domains. Particularly in cystoscopies it is not possibleto produce ground truth depth information to directly train machine learning algorithms for using a monocular image directlyfor depth prediction. This work considers first creating a synthetic cystoscopic environment for initial encoding of depthinformation from synthetically rendered images. Next, the task of predicting pixel-wise depth values for real images is constrainedto a domain adaption between the synthetic and real image domains. This adaptation is done through added gatedresidual blocks in order to simplify the network task and maintain training stability during adversarial training. Training isdone on an internally collected cystoscopy dataset from human patients. The results after training demonstrate the ability topredict reasonable depth estimations from actual cystoscopic videos and added stability from using gated residual blocks isshown to prevent mode collapse during adversarial training.

Introduction of Wright State University Aerospace Medicine Training Program

Betty Somers 한국항공우주의학협회 2012 항공우주의학회지 Vol.22 No.1

Coping with Suffering : An Existentialist Perspective of the 10 Ox herding Pictures

Brian Somers,Song, Yung-Sook 한국선학회 2017 한국선학 Vol.46 No.-

본 연구는 선불교의 “십우도”와 프랑스의 철학자이자 작가인 장 폴 사르트르의 소설 구토에 대한 비교 연구이다. 깨달음의 과정을 10단계로 표현하고 있는 비교적 간결한 십우도와 실존주의적인 고통에 대한 허구적인 일기를 모아 정리한 소설인 구토를 비교함으로써, 각각 새로운 관점에서 해석을 시도해 보았다. 사르트르의 실존주의 입장에서 십우도를 해석할 때, 십우도의 단계가 현대인 또는 현대 사회가 안고 있는 문제가 무엇인지를 짐작할 수 있게 한다. 다른 한편으로, 십우도를 통해서 구토를 해석할 때는, 십우도가 사르트르의 난해한 소설내용을 이해하는데 필요한 중요한 모델을 제공한다. 이 두 이야기의 주인공들은 실존적 존재에 대한 탐구와 물음을 통해 깨달음에 이른다는 점에서 공통점을 가지고 있다. 이 글의 목적은 동서양의 대조적인 두 주인공들의 이야기를 비교하면서 이들이 가지고 있는 실존적 의문과 탐구의 유사성을 강조하는데 있다. 비록 이 두 이야기가 매우 다른 형태로, 서로 다른 시대와 공간에서 쓰여 졌지만 주인공들이 겪는 삶의 고통과 그 고통으로부터 자유와 해방을 향해 나아가는 모습은 인간의 내면에 잠재된 존재에 대한 의문과 자유에 대한 의지의 보편성을 드러낸다고 볼 수 있다. This article is a comparison between the Ten Ox Herding Pictures, a series of paintings and poetry describing the progress toward enlightenment in Seon (Ch’an, Zen) Buddhism, and the novel Nausea by French philosopher, Jean-Paul Sartre. This comparison is done in order to give a fuller understanding to each narrative, particularly emphasizing the ways in which each relate to, and handle existential suffering. It is the aim of this essay to show that both narratives are accounts of a journey from delusion toward awakening by means of an introspective, philosophic investigation. By comparing the Ten Ox Herding Pictures with Nausea each can be seen from a new perspective. When interpreting the Ten Ox Herding Pictures from Sartre’s Existentialist point of view, one is given an example of how the ox-herder’s progression could look in the modern world. By interpreting Nausea through the lens of the Ten Ox Herding Pictures, one is provided with a model to guide them through the complexity of Sartre’s novel. Furthermore, we emphasize the shift from conceptual to non-conceptual understanding that is common to both narratives.

Mahāsatipaṭṭhāna Sutta Influences on the Practices of Mindfulness-Based Cognitive Therapy - Considering the Contributions of Buddhist Theory -

Brian Somers,송영숙 한국불교학회 2021 韓國佛敎學 Vol.98 No.-

Mindfulness-Based Cognitive Therapy (MBCT) aims to use mindfulness meditation to adjust maladaptive thinking routines in order to manage depression by preventing the recurrence and relapse of depressive episodes. It is a secular approach that focuses on guiding participants to reinterpret thoughts and emotions as fluid mental events rather than as fixed concepts. Mindfulness (sati) is a cornerstone of Buddhism, the practices of which are emphasized in The Foundations of Mindfulness (Mahāsatipaṭṭhana Sutta). This paper compares and contrasts the four foundations of mindfulness as described in the Mahāsatipaṭṭhana Sutta with the mindfulness-based practices of MBCT. The purpose of this study is to clarify some of the influences that early Buddhist practice has on MBCT and suggest some of the benefits that would result in MBCT incorporating Buddhist theory more explicitly. The MBCT model alludes to the empty nature of concepts when describing thoughts and emotions as events rather than facts, but it does not take up an ontological investigation of mind or phenomena. This study suggests that MBCT could benefit from such an inquiry, applying impermanence to all objects, not just mental objects. It is further argued that MBCT acts as an introduction to Buddhist psychology however, if it were to explicitly incorporate Buddhist concepts, the program would be more philosophically robust, enabling it to help practitioners to manage depression that is caused not only by maladapted cognition but from suffering (duḥkha) in general.

언어와 공안(公案) 수행 - 지눌(知訥)과 메를로-퐁티(Merleau-Ponty)의 저서에 나타난 제스처 (Gesture)에 대한 연구

( Brian Somers ) 동국대학교 전자불전문화콘텐츠연구소 2021 전자불전 Vol.23 No.-

본 논문의 목적은 화두(話頭)를 중심으로 한 공안(公案) 수행에서 사용되는 비논리적(non-intellectual) 언어에 대한 이해를 증진하고자 함이다. 이때 사용되는 언어는 논리가 모호하고 모순적이며 시(詩)의 구절과 같아 보이고 때로는 일관성이 없으며 어떤 합리적 구조도 갖추고 있지 않은 것처럼 보인다. 그러나 화두를 활용한 수행은 불교 중 특히 선(禪)불교에서 일반적으로 행해지는 수준 높은 수행법으로 이미 정착하였다. 본 논문에서 저자는 지눌(知訥)의 가르침에 따른 화두 수행법을 간략히 소개하고 이 비논리적인 언어가 의사소통의 고차원적 도구가 될 수 있으며 특히 기존의 일반 언어로는 접근할 수 없는 영역의 진리를 탐구하는 데 있어 고도로 발달한 소통 수단이 될 수 있음을 밝히고자 한다. 본 논문의 도입에서는 대륙철학의 관점에서 화두 수행법을 고찰하는 데 있어 지눌 및 메를로-퐁티(Merleau-Ponty)의 존재론적 기초가 특히 언어에 어떻게 적용되는지를 설명한 박진영(Jin. Y. Park)의 연구를 먼저 살펴본다. 이어서 소쉬르(Saussure)의 이론과 소쉬르가 메를로-퐁티에게 미친 영향에 관해 설명한다. 특히 랑그(langue)와 파롤(parole)이라는 두 가지 개념이 메를로-퐁티가 제시한 제스처(gesture)를 설명하는데 있어 갖는 중요성 및 이것이 진리를 밝히는 데 어떤 의미가 있는지를 고찰한다. 나아가 본 논문에서는 이러한 개념을 화두 수행에 적용해 보고, 이들이 화두 수행에서 언어의 역할을 이해하는 데 도움이 된다는 것을 제안하고자 한다. This thesis is an attempt to better understand language as it is used in kong-an (公案, 공안) practice with particular emphasis on hwadu (話頭, 화두). These logically opaque and often contradictory, poem-like stanzas can appear to lack basic structure. However, the practice of hwadu is a well-established and sophisticated practice used commonly in Buddhism, particularly in the Seon (禪, 선) tradition. The aim of this essay is to give a brief account of hwadu practice as taught by Chinul (知訥, 지눌) and show how logically inconsistent language can be a highly developed means of communicating, especially concerning orders of truths that lie beyond conventional linguistics. Investigating hwadu practice through the lens of continental philosophy, this essay begins with the work of Park who accounts for the ontological foundations of Chinul as well as Merleau- Ponty, especially as they apply to language. Following this is an explanation of Saussure and the influence he had on Merleau- Ponty. In particular, “langue” and “parole”, their significance in explaining what Merleau-Ponty means by “gesture” and what that means for the disclosure of truth will be considered. Furthermore, these considerations will be applied to hwadu practice and suggestions made regarding how they are helpful to understanding the role that language plays therein.

Rapid Assessment of Gene Function in the Circadian Clock Using Artificial MicroRNA in Arabidopsis Mesophyll Protoplasts

Kim, J.,Somers, D.E. AMERICAN SOCIETY OF PLANT BIOLOGISTS 2010 Plant Physiology Vol.154 No.2

귀리의 (1-3,1-4)-Beta-Glucanase유전자 발현에 대한 연구 I. 생장 발달중인 귀리의 주요 조직내 Endo-Beta-Glucanase 활성

Yun Song Joong,Somers David A. 한국작물학회 1992 한국작물학회 학술발표대회 논문집 Vol.1992 No.-

System Identification of the Arabidopsis Plant Circadian System

Mathias Foo,David E. Somers,김판준 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.66 No.4

The circadian system generates an endogenous oscillatory rhythm that governs the daily activitiesof organisms in nature. It offers adaptive advantages to organisms through a coordination of theirbiological functions with the optimal time of day. In this paper, a model of the circadian systemin the plant Arabidopsis (species thaliana) is built by using system identification techniques. Priorknowledge about the physical interactions of the genes and the proteins in the plant circadian systemis incorporated in the model building exercise. The model is built by using primarily experimentallyverifieddirect interactions between the genes and the proteins with the available data on mRNAand protein abundances from the circadian system. Our analysis reveals a great performance of themodel in predicting the dynamics of the plant circadian system through the effect of diverse internaland external perturbations (gene knockouts and day-length changes). Furthermore, we found thatthe circadian oscillatory rhythm is robust and does not vary much with the biochemical parametersexcept those of a light-sensitive protein P and a transcription factor TOC1. In other words, thecircadian rhythmic profile is largely a consequence of the network’s architecture rather than itsparticular parameters. Our work suggests that the current experimental knowledge of the geneto-protein interactions in the plant Arabidopsis, without considering any additional hypotheticalinteractions, seems to suffice for system-level modeling of the circadian system of this plant and topresent an exemplary platform for the control of network dynamics in complex living organisms.