969 research outputs found
Towards Optimal Patch Size in Vision Transformers for Tumor Segmentation
Detection of tumors in metastatic colorectal cancer (mCRC) plays an essential
role in the early diagnosis and treatment of liver cancer. Deep learning models
backboned by fully convolutional neural networks (FCNNs) have become the
dominant model for segmenting 3D computerized tomography (CT) scans. However,
since their convolution layers suffer from limited kernel size, they are not
able to capture long-range dependencies and global context. To tackle this
restriction, vision transformers have been introduced to solve FCNN's locality
of receptive fields. Although transformers can capture long-range features,
their segmentation performance decreases with various tumor sizes due to the
model sensitivity to the input patch size. While finding an optimal patch size
improves the performance of vision transformer-based models on segmentation
tasks, it is a time-consuming and challenging procedure. This paper proposes a
technique to select the vision transformer's optimal input multi-resolution
image patch size based on the average volume size of metastasis lesions. We
further validated our suggested framework using a transfer-learning technique,
demonstrating that the highest Dice similarity coefficient (DSC) performance
was obtained by pre-training on training data with a larger tumour volume using
the suggested ideal patch size and then training with a smaller one. We
experimentally evaluate this idea through pre-training our model on a
multi-resolution public dataset. Our model showed consistent and improved
results when applied to our private multi-resolution mCRC dataset with a
smaller average tumor volume. This study lays the groundwork for optimizing
semantic segmentation of small objects using vision transformers. The
implementation source code is available
at:https://github.com/Ramtin-Mojtahedi/OVTPS
Parameter-Efficient Methods for Metastases Detection from Clinical Notes
Understanding the progression of cancer is crucial for defining treatments
for patients. The objective of this study is to automate the detection of
metastatic liver disease from free-style computed tomography (CT) radiology
reports. Our research demonstrates that transferring knowledge using three
approaches can improve model performance. First, we utilize generic language
models (LMs), pretrained in a self-supervised manner. Second, we use a
semi-supervised approach to train our model by automatically annotating a large
unlabeled dataset; this approach substantially enhances the model's
performance. Finally, we transfer knowledge from related tasks by designing a
multi-task transfer learning methodology. We leverage the recent advancement of
parameter-efficient LM adaptation strategies to improve performance and
training efficiency. Our dataset consists of CT reports collected at Memorial
Sloan Kettering Cancer Center (MSKCC) over the course of 12 years. 2,641
reports were manually annotated by domain experts; among them, 841 reports have
been annotated for the presence of liver metastases. Our best model achieved an
F1-score of 73.8%, a precision of 84%, and a recall of 65.8%.Comment: 6 pages, 1 figure, The 36th Canadian Conference on Artificial
Intelligenc
Liver imaging reporting and data system: An expert consensus statement
The increasing incidence and high morbidity and mortality of hepatocellular carcinoma (HCC) have inspired the creation of the Liver Imaging Reporting and Data System (LI-RADS). LI-RADS aims to reduce variability in exam interpretation, improve communication, facilitate clinical therapeutic decisions, reduce omission of pertinent information, and facilitate the monitoring of outcomes. LI-RADS is a dynamic process, which is updated frequently. In this article, we describe the LI-RADS 2014 version (v2014), which marks the second update since the initial version in 2011
Liver imaging : it is time to adopt standardized terminology
Liver imaging plays a vital role in the management of patients at risk for hepatocellular carcinoma (HCC); however, progress in the field is challenged by nonuniform and inconsistent terminology in the published literature. The Steering Committee of the American College of Radiology (ACR)’s Liver Imaging Reporting And Data System (LI-RADS), in conjunction with the LI-RADS Lexicon Writing Group and the LI-RADS International Working Group, present this consensus document to establish a single universal liver imaging lexicon. The lexicon is intended for use in research, education, and clinical care of patients at risk for HCC (i.e., the LI-RADS population) and in the general population (i.e., even when LI-RADS algorithms are not applicable). We anticipate that the universal adoption of this lexicon will provide research, educational, and clinical benefits
Induction of humoral immune response to multiple recombinant Rhipicephalus appendiculatus antigens and their effect on tick feeding success and pathogen transmission
BACKGROUND: Rhipicephalus appendiculatus is the primary vector of Theileria parva, the etiological agent of East Coast fever (ECF), a devastating disease of cattle in sub-Saharan Africa. We hypothesized that a vaccine targeting tick proteins that are involved in attachment and feeding might affect feeding success and possibly reduce tick-borne transmission of T. parva. Here we report the evaluation of a multivalent vaccine cocktail of tick antigens for their ability to reduce R. appendiculatus feeding success and possibly reduce tick-transmission of T. parva in a natural host-tick-parasite challenge model.
METHODS: Cattle were inoculated with a multivalent antigen cocktail containing recombinant tick protective antigen subolesin as well as two additional R. appendiculatus saliva antigens: the cement protein TRP64, and three different histamine binding proteins. The cocktail also contained the T. parva sporozoite antigen p67C. The effect of vaccination on the feeding success of nymphal and adult R. appendiculatus ticks was evaluated together with the effect on transmission of T. parva using a tick challenge model.
RESULTS: To our knowledge, this is the first evaluation of the anti-tick effects of these antigens in the natural host-tick-parasite combination. In spite of evidence of strong immune responses to all of the antigens in the cocktail, vaccination with this combination of tick and parasite antigens did not appear to effect tick feeding success or reduce transmission of T. parva.
CONCLUSION: The results of this study highlight the importance of early evaluation of anti-tick vaccine candidates in biologically relevant challenge systems using the natural tick-host-parasite combination
The quest for the solar g modes
Solar gravity modes (or g modes) -- oscillations of the solar interior for
which buoyancy acts as the restoring force -- have the potential to provide
unprecedented inference on the structure and dynamics of the solar core,
inference that is not possible with the well observed acoustic modes (or p
modes). The high amplitude of the g-mode eigenfunctions in the core and the
evanesence of the modes in the convection zone make the modes particularly
sensitive to the physical and dynamical conditions in the core. Owing to the
existence of the convection zone, the g modes have very low amplitudes at
photospheric levels, which makes the modes extremely hard to detect. In this
paper, we review the current state of play regarding attempts to detect g
modes. We review the theory of g modes, including theoretical estimation of the
g-mode frequencies, amplitudes and damping rates. Then we go on to discuss the
techniques that have been used to try to detect g modes. We review results in
the literature, and finish by looking to the future, and the potential advances
that can be made -- from both data and data-analysis perspectives -- to give
unambiguous detections of individual g modes. The review ends by concluding
that, at the time of writing, there is indeed a consensus amongst the authors
that there is currently no undisputed detection of solar g modes.Comment: 71 pages, 18 figures, accepted by Astronomy and Astrophysics Revie
Identification and functional characterisation of CRK12:CYC9, a novel cyclin-dependent kinase (CDK)-cyclin complex in Trypanosoma brucei
The protozoan parasite, Trypanosoma brucei, is spread by the tsetse fly and causes trypanosomiasis in humans and animals. Both the life cycle and cell cycle of the parasite are complex. Trypanosomes have eleven cdc2-related kinases (CRKs) and ten cyclins, an unusually large number for a single celled organism. To date, relatively little is known about the function of many of the CRKs and cyclins, and only CRK3 has previously been shown to be cyclin-dependent in vivo. Here we report the identification of a previously uncharacterised CRK:cyclin complex between CRK12 and the putative transcriptional cyclin, CYC9. CRK12:CYC9 interact to form an active protein kinase complex in procyclic and bloodstream T. brucei. Both CRK12 and CYC9 are essential for the proliferation of bloodstream trypanosomes in vitro, and we show that CRK12 is also essential for survival of T. brucei in a mouse model, providing genetic validation of CRK12:CYC9 as a novel drug target for trypanosomiasis. Further, functional characterisation of CRK12 and CYC9 using RNA interference reveals roles for these proteins in endocytosis and cytokinesis, respectively
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