89 research outputs found
Distance-Decay Relationship for Biological Wastewater Treatment Plants.
UnlabelledPatterns in the spatial distribution of organisms provide important information about mechanisms underlying biodiversity and the complexity of ecosystems. One of the most well-documented spatial patterns is the distance-decay relationship, which is a universal biogeographic pattern observed repeatedly for plant and animal communities, particularly for microorganisms in natural ecosystems such as soil, ocean, and salt marsh sediment. However, it is uncertain whether the microorganisms exhibit a distance-decay pattern in engineered ecosystems. Therefore, we measured the distance-decay relationship across various microbial functional and phylogenetic groups in 26 biological wastewater treatment plants (WWTPs) in China using a functional gene array (GeoChip 4.2). We found that microbial communities of activated sludge in WWTPs exhibited a significant but very weak distance-decay relationship. The taxon-area z values for different functional and phylogenetic groups were <0.0065, which is about 1 to 2 orders of magnitude lower than those observed in microbial communities elsewhere. Variation-partitioning analysis (VPA) showed that the relationships were driven by both environmental heterogeneity and geographic distance. Collectively, these results provided new insights into the spatial scaling of microbial communities in engineering ecosystems and highlighted the importance of environmental heterogeneity and geographic distance in shaping biogeographic patterns.ImportanceDetermining the distance-decay relationship of microbial biodiversity is important but challenging in microbial ecology. All studies to date are based on natural environments; thus, it remains unclear whether there is such a relationship in an engineered ecosystem. The present study shows that there is a very weak distance-decay relationship in an engineered ecosystem (WWTPs) at the regional-to-continental scale. This study makes fundamental contributions to a mechanistic, predictive understanding of microbial biogeography
Anatomy-Aware Lymph Node Detection in Chest CT using Implicit Station Stratification
Finding abnormal lymph nodes in radiological images is highly important for
various medical tasks such as cancer metastasis staging and radiotherapy
planning. Lymph nodes (LNs) are small glands scattered throughout the body.
They are grouped or defined to various LN stations according to their
anatomical locations. The CT imaging appearance and context of LNs in different
stations vary significantly, posing challenges for automated detection,
especially for pathological LNs. Motivated by this observation, we propose a
novel end-to-end framework to improve LN detection performance by leveraging
their station information. We design a multi-head detector and make each head
focus on differentiating the LN and non-LN structures of certain stations.
Pseudo station labels are generated by an LN station classifier as a form of
multi-task learning during training, so we do not need another explicit LN
station prediction model during inference. Our algorithm is evaluated on 82
patients with lung cancer and 91 patients with esophageal cancer. The proposed
implicit station stratification method improves the detection sensitivity of
thoracic lymph nodes from 65.1% to 71.4% and from 80.3% to 85.5% at 2 false
positives per patient on the two datasets, respectively, which significantly
outperforms various existing state-of-the-art baseline techniques such as
nnUNet, nnDetection and LENS
Parse and Recall: Towards Accurate Lung Nodule Malignancy Prediction like Radiologists
Lung cancer is a leading cause of death worldwide and early screening is
critical for improving survival outcomes. In clinical practice, the contextual
structure of nodules and the accumulated experience of radiologists are the two
core elements related to the accuracy of identification of benign and malignant
nodules. Contextual information provides comprehensive information about
nodules such as location, shape, and peripheral vessels, and experienced
radiologists can search for clues from previous cases as a reference to enrich
the basis of decision-making. In this paper, we propose a radiologist-inspired
method to simulate the diagnostic process of radiologists, which is composed of
context parsing and prototype recalling modules. The context parsing module
first segments the context structure of nodules and then aggregates contextual
information for a more comprehensive understanding of the nodule. The prototype
recalling module utilizes prototype-based learning to condense previously
learned cases as prototypes for comparative analysis, which is updated online
in a momentum way during training. Building on the two modules, our method
leverages both the intrinsic characteristics of the nodules and the external
knowledge accumulated from other nodules to achieve a sound diagnosis. To meet
the needs of both low-dose and noncontrast screening, we collect a large-scale
dataset of 12,852 and 4,029 nodules from low-dose and noncontrast CTs
respectively, each with pathology- or follow-up-confirmed labels. Experiments
on several datasets demonstrate that our method achieves advanced screening
performance on both low-dose and noncontrast scenarios.Comment: MICCAI 202
Continual Segment: Towards a Single, Unified and Accessible Continual Segmentation Model of 143 Whole-body Organs in CT Scans
Deep learning empowers the mainstream medical image segmentation methods.
Nevertheless current deep segmentation approaches are not capable of
efficiently and effectively adapting and updating the trained models when new
incremental segmentation classes (along with new training datasets or not) are
required to be added. In real clinical environment, it can be preferred that
segmentation models could be dynamically extended to segment new organs/tumors
without the (re-)access to previous training datasets due to obstacles of
patient privacy and data storage. This process can be viewed as a continual
semantic segmentation (CSS) problem, being understudied for multi-organ
segmentation. In this work, we propose a new architectural CSS learning
framework to learn a single deep segmentation model for segmenting a total of
143 whole-body organs. Using the encoder/decoder network structure, we
demonstrate that a continually-trained then frozen encoder coupled with
incrementally-added decoders can extract and preserve sufficiently
representative image features for new classes to be subsequently and validly
segmented. To maintain a single network model complexity, we trim each decoder
progressively using neural architecture search and teacher-student based
knowledge distillation. To incorporate with both healthy and pathological
organs appearing in different datasets, a novel anomaly-aware and confidence
learning module is proposed to merge the overlapped organ predictions,
originated from different decoders. Trained and validated on 3D CT scans of
2500+ patients from four datasets, our single network can segment total 143
whole-body organs with very high accuracy, closely reaching the upper bound
performance level by training four separate segmentation models (i.e., one
model per dataset/task)
Matching in the Wild: Learning Anatomical Embeddings for Multi-Modality Images
Radiotherapists require accurate registration of MR/CT images to effectively
use information from both modalities. In a typical registration pipeline, rigid
or affine transformations are applied to roughly align the fixed and moving
images before proceeding with the deformation step. While recent learning-based
methods have shown promising results in the rigid/affine step, these methods
often require images with similar field-of-view (FOV) for successful alignment.
As a result, aligning images with different FOVs remains a challenging task.
Self-supervised landmark detection methods like self-supervised Anatomical
eMbedding (SAM) have emerged as a useful tool for mapping and cropping images
to similar FOVs. However, these methods are currently limited to intra-modality
use only. To address this limitation and enable cross-modality matching, we
propose a new approach called Cross-SAM. Our approach utilizes a novel
iterative process that alternates between embedding learning and CT-MRI
registration. We start by applying aggressive contrast augmentation on both CT
and MRI images to train a SAM model. We then use this SAM to identify
corresponding regions on paired images using robust grid-points matching,
followed by a point-set based affine/rigid registration, and a deformable
fine-tuning step to produce registered paired images. We use these registered
pairs to enhance the matching ability of SAM, which is then processed
iteratively. We use the final model for cross-modality matching tasks. We
evaluated our approach on two CT-MRI affine registration datasets and found
that Cross-SAM achieved robust affine registration on both datasets,
significantly outperforming other methods and achieving state-of-the-art
performance
CancerUniT: Towards a Single Unified Model for Effective Detection, Segmentation, and Diagnosis of Eight Major Cancers Using a Large Collection of CT Scans
Human readers or radiologists routinely perform full-body multi-organ
multi-disease detection and diagnosis in clinical practice, while most medical
AI systems are built to focus on single organs with a narrow list of a few
diseases. This might severely limit AI's clinical adoption. A certain number of
AI models need to be assembled non-trivially to match the diagnostic process of
a human reading a CT scan. In this paper, we construct a Unified Tumor
Transformer (CancerUniT) model to jointly detect tumor existence & location and
diagnose tumor characteristics for eight major cancers in CT scans. CancerUniT
is a query-based Mask Transformer model with the output of multi-tumor
prediction. We decouple the object queries into organ queries, tumor detection
queries and tumor diagnosis queries, and further establish hierarchical
relationships among the three groups. This clinically-inspired architecture
effectively assists inter- and intra-organ representation learning of tumors
and facilitates the resolution of these complex, anatomically related
multi-organ cancer image reading tasks. CancerUniT is trained end-to-end using
a curated large-scale CT images of 10,042 patients including eight major types
of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D
tumor masks annotated by radiologists). On the test set of 631 patients,
CancerUniT has demonstrated strong performance under a set of clinically
relevant evaluation metrics, substantially outperforming both multi-disease
methods and an assembly of eight single-organ expert models in tumor detection,
segmentation, and diagnosis. This moves one step closer towards a universal
high performance cancer screening tool.Comment: ICCV 2023 Camera Ready Versio
Global diversity and biogeography of bacterial communities in wastewater treatment plants
Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes
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