1,157 research outputs found
Editorial: orchid genomics and developmental biology
Orchidaceae is the second largest family of flowering plants with more than 27,000 species inhabiting nearly every habitat worldwide. Orchids exhibit an exceptional
morphological and ecological diversity, and are highly valued on the global horticultural
market. Orchids possess unique morphological and physiological characteristics, such as
highly reduced seeds with an immature embryo, complex flower structures such as the
gynandrium and labellum, and have evolved crassulacean acid metabolism and
mycoheterotrophy multiple times independently. This range of traits renders orchids
prime non-model plants for studying different aspects of evolution through mechanistic
studies considering gene function, physiology, and phylogenetic relationships. As
summarized below, this Research Topic presents recent advances in orchid biology
and consists of 12 publications in the fields of reproductive development, evolution,
biotechnology, and photosynthesis
Editorial: Orchid genomics and developmental biology, volume II
[Extract] Orchidaceae constitute the second-largest flowering plant family worldwide with over 27,000 species found on all continents except Antarctica. Orchids are frequently celebrated for their exceptional morphological and ecological diversity and are highly valued in the horticultural trade. Orchids exhibit distinct floral and physiological features, such as fused male and female flower parts forming the gynostemium, a floral lip often adorned with calli, glands, spurs, and distinctive color patterns, and the crassulacean acid metabolism (CAM), a water-saving physiological pathway which has evolved multiple times independently within the family. Orchids possess highly specialized ecological relationships, such as often species-specific plant-pollinator interactions including food- and sexual deception and dependence
on mycorrhizal fungi for germination of their minute seed
In Vitro Organogenesis of a Slipper Orchid, Paphiopedilum ‘Alma Gavaert’
The aim of the present study was to improve the regeneration efficiency of callus lines in a slipper orchid, Paphiopedilum ‘Alma Gavaert’. Three kinds of vegetative tissues, root, stem and leaf segments, were used as explants to induce callogenesis; out of these, only root explants formed callus and was subcultured in the presence of 5 mg/L dicamba and 5 mg/L 2,4-D combined with 1 or 2 mg/L TDZ. The resulting four callus lines, assigned as 5Di1T, 5Di2T, 5D1T and 5D2T, respectively, were used to test the effect of NAA to BA ratios on re-differentiation, wherein the highest number of shoots (approximately 2 shoots/0.1 g callus clump) were obtained in callus line 5D2T at ratios of 0.001 and 0.002. A largely improvement of shoot regeneration efficiency was obtained by continuous selection of callus lines which derived from different explant positions. Eventually, six callus lines, including 5D2T-T6-G5 to 5D2T-T6-G10, were able to produce approximately 10 times of shoots per callus clump when compared with the parental callus line 5D2T
A Novel Confidence Induced Class Activation Mapping for MRI Brain Tumor Segmentation
Magnetic resonance imaging (MRI) is a commonly used technique for brain tumor
segmentation, which is critical for evaluating patients and planning treatment.
To make the labeling process less laborious and dependent on expertise,
weakly-supervised semantic segmentation (WSSS) methods using class activation
mapping (CAM) have been proposed. However, current CAM-based WSSS methods
generate the object localization map using internal neural network information,
such as gradient or trainable parameters, which can lead to suboptimal
solutions. To address these issues, we propose the confidence-induced CAM
(Cfd-CAM), which calculates the weight of each feature map by using the
confidence of the target class. Our experiments on two brain tumor datasets
show that Cfd-CAM outperforms existing state-of-the-art methods under the same
level of supervision. Overall, our proposed Cfd-CAM approach improves the
accuracy of brain tumor segmentation and may provide valuable insights for
developing better WSSS methods for other medical imaging tasks
Ultrasonication-Assisted Spray Ionization Mass Spectrometry for the Analysis of Biomolecules in Solution
In this paper, we describe a novel technique—ultrasonication-assisted spray ionization (UASI)—for the generation of singly charged and multiply charged gas-phase ions of biomolecules (e.g., amino acids, peptides, and proteins) from solution; this method employs a low-frequency ultrasonicator (ca. 40 kHz) in place of the high electric field required for electrospray ionization. When a capillary inlet is immersed into a sample solution within a vial subjected to ultrasonication, the solution is continually directed to the capillary outlet as a result of ultrasonication-assisted capillary action; an ultrasonic spray of the sample solution is emitted at the outlet of the tapered capillary, leading to the ready generation of gas-phase ions. Using an ion trap mass spectrometer, we found that singly charged amino acid and multiply charged peptides/proteins ions were generated through this single-step operation, which is both straightforward and extremely simple to perform. The setup is uncomplicated: only a low-frequency ultrasonicator and a tapered capillary are required to perform UASI. The mass spectra of the multiply charged peptides and proteins obtained from sample solutions subjected to UASI resemble those observed in ESI mass spectra
AME-CAM: Attentive Multiple-Exit CAM for Weakly Supervised Segmentation on MRI Brain Tumor
Magnetic resonance imaging (MRI) is commonly used for brain tumor
segmentation, which is critical for patient evaluation and treatment planning.
To reduce the labor and expertise required for labeling, weakly-supervised
semantic segmentation (WSSS) methods with class activation mapping (CAM) have
been proposed. However, existing CAM methods suffer from low resolution due to
strided convolution and pooling layers, resulting in inaccurate predictions. In
this study, we propose a novel CAM method, Attentive Multiple-Exit CAM
(AME-CAM), that extracts activation maps from multiple resolutions to
hierarchically aggregate and improve prediction accuracy. We evaluate our
method on the BraTS 2021 dataset and show that it outperforms state-of-the-art
methods.Comment: arXiv admin note: text overlap with arXiv:2306.0547
Conditional Diffusion Models for Weakly Supervised Medical Image Segmentation
Recent advances in denoising diffusion probabilistic models have shown great
success in image synthesis tasks. While there are already works exploring the
potential of this powerful tool in image semantic segmentation, its application
in weakly supervised semantic segmentation (WSSS) remains relatively
under-explored. Observing that conditional diffusion models (CDM) is capable of
generating images subject to specific distributions, in this work, we utilize
category-aware semantic information underlied in CDM to get the prediction mask
of the target object with only image-level annotations. More specifically, we
locate the desired class by approximating the derivative of the output of CDM
w.r.t the input condition. Our method is different from previous diffusion
model methods with guidance from an external classifier, which accumulates
noises in the background during the reconstruction process. Our method
outperforms state-of-the-art CAM and diffusion model methods on two public
medical image segmentation datasets, which demonstrates that CDM is a promising
tool in WSSS. Also, experiment shows our method is more time-efficient than
existing diffusion model methods, making it practical for wider applications
A Novel In Vitro
An alternative in vitro protocol for embryo induction directly from intact living seedlings of Phalaenopsis aphrodite subspecies formosana was established in this study. Without the supplementation of plant growth regulators (PGRs), no embryos were obtained from all the seedlings when cultured on the solid medium. In contrast, embryos formed from the seedlings on the 2-layer medium and the 2-step culture system without the use of PGRs. It was found that the age of the seedlings affected embryo induction. The 2-month-old seedlings typically had higher embryogenic responses when compared with the 4-month-old seedlings in the 2-layer medium or 2-step system. For the 2-month-old seedlings, 1 mg/L TDZ resulted in the highest number of embryos at the distal site of the shoot. However, on the leaves’ surface, 0.5 mg/L TDZ induced the highest number of embryos. When the 2-month-old seedlings were cultured using the 2-step method at 1 mg/L of TDZ, the highest embryogenic response was obtained, with an average of 44 embryos formed on each seedling. These adventitious embryos were able to convert into plantlets in a PGR-free 1/2 MS medium, and the plantlets had normal morphology and growth
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