Fully Automatic Karyotyping via Deep Convolutional Neural Networks

Chromosome karyotyping is an important yet labor-intensive procedure for diagnosing genetic diseases. Automating such a procedure drastically reduces the manual work of cytologists and increases congenital disease diagnosing precision. Researchers have contributed to chromosome segmentation and classification for decades. However, very few studies integrate the two tasks as a unified, fully automatic procedure or achieved a promising performance. This paper addresses the gap by presenting: 1) A novel chromosome segmentation module named ChrRender, with the idea of rendering the chromosome instances by combining rich global features from the backbone and coarse mask prediction from Mask R-CNN; 2) A devised chromosome classification module named ChrNet4 that pays more attention to channel-wise dependencies from aggregated informative features and calibrating the channel interdependence; 3) An integrated Render-Attention-Architecture to accomplish fully automatic karyotyping with segmentation and classification modules; 4) A strategy for eliminating differences between training data and segmentation output data to be classified. These proposed methods are implemented in three ways on the public Q-band BioImLab dataset and a G-band private dataset. The results indicate promising performance: 1) on the joint karyotyping task, which predicts a karyotype image by first segmenting an original microscopical image, then classifying each segmentation output with a precision of 89.75% and 94.22% on the BioImLab and private dataset, respectively; 2) On the separate task with two datasets, ChrRender obtained AP50 of 96.652% and 96.809% for segmentation, ChrNet4 achieved 95.24% and 94.07% for classification, respectively. The COCO format annotation files of BioImLab used in this paper are available at https://github.com/Alex17swim/BioImLab The study introduces an integrated workflow to predict a karyotyping image from a Microscopical Chromosome Image. With state-of-the-art performance on a public dataset, the proposed Render-Attention-Architecture has accomplished fully automatic chromosome karyotyping

A Built-In Strategy for Containment of Transgenic Plants: Creation of Selectively Terminable Transgenic Rice

Plant transgenic technology has been widely utilized for engineering crops for trait improvements and for production of high value proteins such as pharmaceuticals. However, the unintended spreading of commercial transgenic crops by pollination and seed dispersal is a major concern for environmental and food safety. Simple and reliable containment strategies for transgenes are highly desirable. Here we report a novel method for creating selectively terminable transgenic rice. In this method, the gene(s) of interest is tagged with a RNA interference cassette, which specifically suppresses the expression of the bentazon detoxification enzyme CYP81A6 and thus renders transgenic rice to be sensitive to bentazon, a herbicide used for rice weed control. We generated transgenic rice plants by this method using a new glyphosate resistant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene from Pesudomonas putida as the gene of interest, and demonstrated that these transgenic rice plants were highly sensitive to bentazon but tolerant to glyphosate, which is exactly the opposite of conventional rice. Field trial of these transgenic rice plants further confirmed that they can be selectively killed at 100% by one spray of bentazon at a regular dose used for conventional rice weed control. Furthermore, we found that the terminable transgenic rice created in this study shows no difference in growth, development and yield compared to its non-transgenic control. Therefore, this method of creating transgenic rice constitutes a novel strategy of transgene containment, which appears simple, reliable and inexpensive for implementation

Open educational resources in China : a governmentality analysis

Using a sociological approach, this study examines China’s reform of open educational resources (OER), which has prompted significant changes to the nation’s higher education sector. Through an analysis of the policy processes that have driven the reform, this study demonstrates that the reform has involved and brought significant changes to its participants as resource administrators, providers, and receivers. By using governmentality as a poststructuralist analytical framework, this study shows the particular ways in which the reform process has been governed and the ways in which the governing practices have changed the conduct of higher education. The study reveals the power relations exercised through the reform and offers a critique of China’s higher education sector

The Dual-Challenge of Teaching Online in a Foreign Land: Understanding Western Foreign Teachers’ Professional Identity and Confidence Development via a Transformative Learning Lens

This study takes a transformative learning lens to gain insights into Western foreign teachers’ identity as educators and professional confidence in online teaching at a Sino-British university. The biographical narrative interpretive method was used for data collection and analysis. The researcher gathered critical incidents during the pandemic through in-depth interviews with six Western foreign teachers. Western foreign teachers encountered dual-dimensional challenges: one related to cultural differences in teaching and the other caused by a shift to online teaching. Western foreign teachers’ belief in their professional identity as educators anchored by their pedagogical and curricular rationales helped them overcome workplace challenges. Through action-taking and critically reflecting on their experiences, Western foreign teachers gained skills and competencies that promoted their confidence in transnational education. This study developed a framework to explain teacher identity as educators and professional confidence development in teaching as an iterative process led by transformative learning. The reflective practice serves as a medium to help Western foreign teachers construct experiences in unfamiliar situations. The study makes a practical contribution to understanding Western foreign teachers’ professional development, which can be used for recruitment and retention

Examining gains and pains of a new virtual internship design

This study investigated how student effort and the course design influenced an online internship in China. A cohort of 95 postgraduate students became distance learners in a credit-bearing internship course due to COVID-19. The course leader applied the action learning framework to prompt student online collaboration and group inquiry. The framework assumes the importance of self-reliant learner autonomy in virtual internships. After the course, researchers analyzed the effects of self-directed learning with technology on a multidimensional community of inquiry in a virtual environment. The study also identified students’ narratives that explain how self-directed learning with technology interacted with three elements of virtual communities of inquiry: social, cognitive, and teaching. Findings explain how virtual internships can be facilitated through a community of inquiry model. Educators and practitioners may consider the model to demonstrate student-staff partnerships (Fitzgerald et al., 2020) to achieve quality transformation of internships from face-to-face mode to distance education.</p

RT-PCR analysis of <i>CYP81A6</i> mRNA abundance in transgenic and non-transgenic rice.

<p>The rice <i>Actin</i> gene was used as the control. M, DNA size maker; CK, non-transgenic rice; R450-2, R450-5, R450-6 and R450-7 are independent transgenic events sensitive to bentazon.</p

Comparison of agronomic traits between the terminable transgenic rice and its non-transgenic control in field trial.

<p>Control plants are non-transgenic rice of the same cultivar as the transgenic plants. R450-2 and R450-5 are two independent transgenic events.</p

Field trial for selective termination of the transgenic rice.

<p>The T₁ transgenic plants and the conventional control rice plants were sprayed with Bentazon at 1500 mg/L. The picture was taken 7 days after the spray. CK, conventional rice; R450-2 and R450-5 are T₁ transgenic rice plants of the event R450-2 and R450-5, respectively. The surviving plants in the R450-2 rows were segregates not carrying the transgene.</p