Simple low-cost approaches to semantic segmentation in radiation therapy planning for prostate cancer using deep learning with non-contrast planning CT images

PurposeDeep learning has shown great efficacy for semantic segmentation. However, there are difficulties in the collection, labeling and management of medical imaging data, because of ethical complications and the limited number of imaging studies available at a single facility.This study aimed to find a simple and low-cost method to increase the accuracy of deep learning semantic segmentation for radiation therapy of prostate cancer.MethodsIn total, 556 cases with non-contrast CT images for prostate cancer radiation therapy were examined using a two-dimensional U-Net. Initially, all slices were used for the input data. Then, we removed slices of the cranial portions, which were beyond the margins of the bladder and rectum. Finally, the ground truth labels for the bladder and rectum were added as channels to the input for the prostate training dataset.ResultsThe highest mean dice similarity coefficients (DSCs) for each organ in the test dataset of 56 cases were 0.85 ± 0.05, 0.94 ± 0.04 and 0.85 ± 0.07 for the prostate, bladder and rectum, respectively. Removal of the cranial slices from the original images significantly increased the DSC of the rectum from 0.83 ± 0.09 to 0.85 ± 0.07 (p < 0.05). Adding bladder and rectum information to prostate training without removing the slices significantly increased the DSC of the prostate from 0.79 ± 0.05 to 0.85 ± 0.05 (p < 0.05).ConclusionsThese cost-free approaches may be useful for new applications, which may include updated models and datasets. They may be applicable to other organs at risk (OARs) and clinical targets such as elective nodal irradiation.     

基于文献计量学的百合属植物研究态势分析

基于Web of Science（简称WoS）核心数据库检索了1998-2018年间百合属植物文献,利用CiteSpace软件从国家、机构、作者、期刊以及高被引文章等方面进行了文献计量学统计分析。1998-2018年间共发表百合属植物文章1 058篇,2006年后中国发表文章数量居榜首并呈波动增长,中国科学院发表的文章数量在研究机构中排名第一。排名前2位的作者均来自荷兰瓦赫宁根大学。发文量及影响力最大的期刊是Scientia Horticulturae。发文量前10位的研究百合属植物的文章80%属于基础科学和技术科学,研究热点集中于形态学、细胞和分子生物学方向。近5年被引频次最多的高被引论文集中在百合属植物活性物质的功能验证、活性成分及其在营养健康方面的功效等方向,这些领域成为百合属植物研究的新趋势。     

基于非核糖体肽的文献计量分析

许多临床上的重要抗生素来源于微生物生产的非核糖体肽类天然产物或者聚酮-非核糖体肽杂合体类天然产物,本文选取了近5年Web of Science上关于非核糖体肽的国际期刊文献,采用文献计量、统计分析等方法展示非核糖体肽研究领域的热点方向,探究了该领域的发展趋势,以期为进一步研究提供参考。     

Psychological and physiological effect in humans of touching plant foliage - using the semantic differential method and cerebral activity as indicators

Background

Numerous studies have reported on the healing powers of plants and nature, but there have not been so many instances of experimental research. In particular, there are very few psychological and physiological studies using tactile stimuli. This study examines the psychological and physiological effects of touching plant foliage by using an evaluation profile of the subjects’ impressions and investigating cerebral blood flow.

Methods

The subjects were 14 young Japanese men aged from 21 to 27 years (mean ± standard deviation: 23.6 ± 2.4). With their eyes closed, the subjects touched four different tactile samples including a leaf of natural pothos (Epipremnum aureum). The physiological indices were compared before and after each stimulus. Psychological indices were obtained using a ‘semantic differential’ method.

Results

The fabric stimulus gave people ‘soft’ and ‘rough’ impressions, ‘kind’, ‘peaceful’ and ‘pleasant’ feelings psychologically, and a sense of physiological calm. On the other hand, the metal stimulus gave people ‘cold’, ‘smooth’ and ‘hard’ impressions and an image of something ‘artificial’. The metal stimulus caused a stress response in human cerebral blood flow although its evaluation in terms of ‘pleasant or unpleasant’ was neutral. There were no remarkable differences between the stimuli of natural and artificial pothos compared with other types of stimulus psychologically. However, only the natural pothos stimulus showed a sense of physiological calm in the same appearance as the fabric stimulus.

Conclusions

This study shows that people experience an unconscious calming reaction to touching a plant. It is to be concluded that plants are an indispensable element of the human environment.     

Metabolomics standards initiative: ontology working group work in progress

In this article we present the activities of the Ontology Working Group (OWG) under the Metabolomics Standards Initiative (MSI) umbrella. Our endeavour aims to synergise the work of several communities, where independent activities are underway to develop terminologies and databases for metabolomics investigations. We have joined forces to rise to the challenges associated with interpreting and integrating experimental process and data across disparate sources (software and databases, private and public). Our focus is to support the activities of the other MSI working groups by developing a common semantic framework to enable metabolomics-user communities to consistently annotate the experimental process and to enable meaningful exchange of datasets. Our work is accessible via a public webpage and a draft ontology has been posted under the Open Biological Ontology umbrella. At the very outset, we have agreed to minimize duplications across omics domains through extensive liaisons with other communities under the OBO Foundry. This is work in progress and we welcome new participants willing to volunteer their time and expertise to this open effort. See the MSI Ontology Working Group website for a complete list of members and contributors. Web URL:     

蛛网和蛛体挥发物诱导的阴暗拟隙蛛（蜘蛛目：漏斗蛛科）种内选择偏好行为

化学通讯是蜘蛛类群普遍使用的种内和种间信息交流方式,极可能是蜘蛛进化过程中最初用来进行个体之间信息交流的途径。本研究利用双向选择系统,测试了阴暗拟隙蛛(Pireneitega luctuosa)对同种其他个体的蛛网和蛛体挥发物的选择行为,采用卡方检验的统计学方法、利用SPSS 19.0和Origin Pro 8等软件对所测蜘蛛的选择数据进行了分析。结果显示:①阴暗拟隙蛛雄蛛和雌蛛对来自同种异性的蛛网(P 0.001)和蛛体挥发物(P 0.05)均具有显著的趋向性,雌、雄蛛在异性蛛网或蛛体挥发物所在的选择盒表现更长时间的停留、探索、织网等行为;②雄蛛和雌蛛对幼蛛蛛体释放出来的挥发物均表现出显著的回避行为(P 0.05),倾向于远离具有幼蛛挥发物的选择盒;③幼蛛对同种幼蛛和雄蛛的蛛网(P 0.001)以及同种幼蛛的蛛体挥发物(P 0.05)均具有选择偏好性,说明幼蛛倾向于与同种个体接近。我们的研究表明,阴暗拟隙蛛雄蛛、雌蛛及幼蛛的蛛网和蛛体挥发物能诱导种内其他个体的趋向或回避行为,阴暗拟隙蛛幼蛛对同种幼蛛的选择偏好性可能是该种个体在同一地域聚集分布的主要原因。我们的研究从行为学角度证实,阴暗拟隙蛛的蛛网及体表均携带有能够标识其性别和龄期的相关信息化学物质。     

Howard Pattee's theoretical biology--a radical epistemological stance to approach life, evolution and complexity

This paper offers a short review of Pattee's main contributions to science and philosophy. With no intention of being exhaustive, an account of Pattee's work is presented which discusses some of his ideas and their reception. This is done through an analysis centered in what is thought to be his main contribution: the elaboration of an internal epistemic stance to better understand life, evolution and complexity. Having introduced this core idea as a sort of a posteriori cohesive element of a complex but highly coherent and complete system of thinking, further specific elements are also reviewed.     

HOMSTRAD: a database of protein structure alignments for homologous families.

We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X-ray analysis and accuracy of the structure. For each family, the database provides a structure-based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www-cryst.bioc.cam. ac.uk/-homstrad/, with search facilities and links to other databases.