AutoKary2022: A Large-Scale Densely Annotated Dateset for Chromosome Instance Segmentation

Automated chromosome instance segmentation from metaphase cell microscopic images is critical for the diagnosis of chromosomal disorders (i.e., karyotype analysis). However, it is still a challenging task due to lacking of densely annotated datasets and the complicated morphologies of chromosomes, e.g., dense distribution, arbitrary orientations, and wide range of lengths. To facilitate the development of this area, we take a big step forward and manually construct a large-scale densely annotated dataset named AutoKary2022, which contains over 27,000 chromosome instances in 612 microscopic images from 50 patients. Specifically, each instance is annotated with a polygonal mask and a class label to assist in precise chromosome detection and segmentation. On top of it, we systematically investigate representative methods on this dataset and obtain a number of interesting findings, which helps us have a deeper understanding of the fundamental problems in chromosome instance segmentation. We hope this dataset could advance research towards medical understanding. The dataset can be available at: https://github.com/wangjuncongyu/chromosome-instance-segmentation-dataset.Comment: Accepted by ICME 202

Surface passivation of random alloy AlGaAsSb avalanche photodiode

AlGaAsSb attracts significant interest for near‐infrared avalanche photodiodes (APD). The authors report a two‐order reduction in the dark current and a six‐time enhancement of gain in random alloy (RA) AlGaAsSb APD that is surface passivated by conformal coating of Al2O3 via atomic layer deposition (ALD). The dark currents of the APDs with 400‐µm diameter (dry etched) at 90% breakdown voltage (0.9 Vbr) are (5.5 ± 0.5) × 10−5 A, (2.1 ± 0.4) × 10−5 A, and (6.2 ± 0.8) × 10−7 A for non‐passivated, Si3N4 passivated, and Al2O3 passivated devices, respectively. The dark current at a gain of 10 for the Al2O3 passivated device is 1 × 10−8 A which is comparable to the reported value for 100‐µm diameter mesa diodes passivated by SU‐8. Maximum gain values of 6, 12, and 35 were obtained for non‐passivated, Si3N4 passivated, and Al2O3 passivated devices, respectively. Moreover, punch‐through capacitance of 8 pF in a spectral response of 450 to 850 nm was obtained. Thus, Al2O3 passivation can be the best solution for antimonide optoelectronic devices

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Opportunities and Challenges of Designing Assistive Technologies for Aphasia Patients in Singapore: The Case of a Speech Evaluation Prototype

Aphasia is a language disorder caused by brain damage, resulting in difficulties with speaking, understanding, reading, and writing. This study focuses on addressing challenges faced by local therapists in aphasia treatment. Through an ethnographic study involving observations and interviews, critical issues in current technological solutions for aphasia treatment were identified. These issues include the lack of feedback during patient training, limited localized content, repetitive materials, and a lack of options for conversational speech training. In our study, we tried to address one of these issues concerning automatic evaluation of patient speech pronunciation. By utilizing public datasets and local patient data, we developed a system that provides accurate pronunciation scores and personalized feedback, assisting therapists in guiding patient progress. The system supports customized pronunciations, including local accents and dialects. The system is designed for multiple platforms, ensuring accessibility, and can be extended to involve speech therapists to enhance its capabilities. This study emphasizes the importance of integrating research insights with clinical practice, empowering therapists, and enhancing the quality of aphasia treatment

C2FResMorph:A high-performance framework for unsupervised 2D medical image registration

Deformable medical image registration is an important precursor task for surgical automation, while enhancing the registration performance of 2D medical images remains a challenging work. Existing methods primarily minimize the similarity loss between image pairs as the main optimization objective, leading to limited registration accuracy and a lack of pixel matching. Moreover, the scarcity of informative features in 2D images often results in overfitting on the training set, hampering generalization. To address these issues, we propose C2FResMorph, a learning-based deformable registration algorithm specifically designed for 2D medical images. C2FResMorph employs a two-stage framework that improves registration accuracy and preserves topology during deformation in a coarse-to-fine manner. Inside the framework, by leveraging the convolutional neural network's locality and the multi-head self-attention mechanism's globality, a ResMorph registration network is designed. Additionally, the integration of residual image knowledge addresses deformation folding in 2D image registration, enhancing the preservation of local structures and improving generalization. Experimental evaluations on three datasets demonstrate that C2FResMorph outperforms existing learning-based methods in terms of accuracy, generalization ability for 2D medical image registration, and also retains the efficiency advantages.</p

Genome-Wide Identification of <i>AP2/ERF</i> Superfamily Genes in <i>Juglans mandshurica</i> and Expression Analysis under Cold Stress

Juglans mandshurica has strong freezing resistance, surviving temperatures as low as −40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT-PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species

A Comprehensive Review on Silk Fibroin as a Persuasive Biomaterial for Bone Tissue Engineering

Bone tissue engineering (BTE) utilizes a special mix of scaffolds, cells, and bioactive factors to regulate the microenvironment of bone regeneration and form a three-dimensional bone simulation structure to regenerate bone tissue. Silk fibroin (SF) is perhaps the most encouraging material for BTE given its tunable mechanical properties, controllable biodegradability, and excellent biocompatibility. Numerous studies have confirmed the significance of SF for stimulating bone formation. In this review, we start by introducing the structure and characteristics of SF. After that, the immunological mechanism of SF for osteogenesis is summarized, and various forms of SF biomaterials and the latest development prospects of SF in BTE are emphatically introduced. Biomaterials based on SF have great potential in bone tissue engineering, and this review will serve as a resource for future design and research