Differential cell counts using center-point networks achieves human-level accuracy and efficiency over segmentation.
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ABSTRACT:
SUBMITTER: Lee SMW
PROVIDER: S-EPMC8377024 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundPoint-of-care (PoC) testing of platelet count (PLT) provides real-time data for rapid decision making. The goal of this study is to evaluate the accuracy and precision of platelet counting using a new microvolume (8 μL), absolute counting, 1.5 kg cytometry-based blood analyzer, the rHEALTH ONE (rHEALTH) in comparison with the International Society of Laboratory Hematology (ISLH) platelet method, which uses a cytometer and an impedance analyzer.MethodsInclusion eligibility were healthy adults (M/F) ages 18-80 for donation of fingerprick and venous blood samples. Samples were from a random N = 31 volunteers from a single U.S. site. Samples were serially diluted to test thrombocytopenic ranges. Interfering substances and conditions were tested, including RBC fragments, platelet fragments, cholesterol, triglycerides, lipids, anti-platelet antibodies, and temperature.ResultsThe concordance between the rHEALTH and ISLH methods had a slope = 1.030 and R2 = 0.9684. The rHEALTH method showed a correlation between capillary and venous blood samples (slope = 0.9514 and R2 = 0.9684). Certain interferents changed platelet recovery: RBC fragments and anti-platelet antibodies with the ISLH method; platelet fragments and anti-platelet antibodies on the rHEALTH; and RBC fragments, platelets fragments, triglycerides and LDL on the clinical impedance analyzer. The rHEALTH's precision ranged from 3.1-8.0%, and the ISLH from 1.0-10.5%.ConclusionsThe rHEALTH method provides similar results with the reference method and good correlation between adult capillary and venous blood samples. This demonstrates the ability of the rHEALTH to provide point-of-care assessment of normal and thrombocytopenic platelet counts from fingerprick blood with high precision and limited interferences.
| S-EPMC8389400 | biostudies-literature
Project description:BackgroundHistone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson distribution to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them.ResultsOur comparisons on seven reference datasets of histone modifications (H3K36me3 & H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model with alternative noise assumptions and supervised learning of the penalty parameter reduces the over-dispersion exhibited by count data. These models, implemented in the R package CROCS ( https://github.com/aLiehrmann/CROCS ), detect the peaks more accurately than algorithms which rely on natural assumptions.ConclusionThe segmentation models we propose can benefit researchers in the field of epigenetics by providing new high-quality peak prediction tracks for H3K36me3 and H3K4me3 histone modifications.
| S-EPMC8201703 | biostudies-literature
Project description:Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction of the secondary structures is widely studied. Our previous research shows that cutting long sequences into shorter chunks, predicting secondary structures of the chunks independently using thermodynamic methods, and reconstructing the entire secondary structure from the predicted chunk structures can yield better accuracy than predicting the secondary structure using the RNA sequence as a whole. The chunking, prediction, and reconstruction processes can use different methods and parameters, some of which produce more accurate predictions than others. In this paper, we study the prediction accuracy and efficiency of three different chunking methods using seven popular secondary structure prediction programs that apply to two datasets of RNA with known secondary structures, which include both pseudoknotted and non-pseudoknotted sequences, as well as a family of viral genome RNAs whose structures have not been predicted before. Our modularized MapReduce framework based on Hadoop allows us to study the problem in a parallel and robust environment.On average, the maximum accuracy retention values are larger than one for our chunking methods and the seven prediction programs over 50 non-pseudoknotted sequences, meaning that the secondary structure predicted using chunking is more similar to the real structure than the secondary structure predicted by using the whole sequence. We observe similar results for the 23 pseudoknotted sequences, except for the NUPACK program using the centered chunking method. The performance analysis for 14 long RNA sequences from the Nodaviridae virus family outlines how the coarse-grained mapping of chunking and predictions in the MapReduce framework exhibits shorter turnaround times for short RNA sequences. However, as the lengths of the RNA sequences increase, the fine-grained mapping can surpass the coarse-grained mapping in performance.By using our MapReduce framework together with statistical analysis on the accuracy retention results, we observe how the inversion-based chunking methods can outperform predictions using the whole sequence. Our chunk-based approach also enables us to predict secondary structures for very long RNA sequences, which is not feasible with traditional methods alone.
| S-EPMC3952952 | biostudies-literature
Project description:Multi-atlas brain segmentation of human brain MR images allows quantification research in structural neuroimaging. To achieve high accuracy and computational efficiency of segmentation relies on a custom subset of atlases for each target subject. However, the criterion for atlas pre-selection remains an open question. In this study, two atlas pre-selection approaches based on location-based feature matching were proposed and compared to random and mutual information-based methods using a database of 47 atlases. A varying number of atlases ranked top with hierarchical structural granularity were compared using Dice overlap. The results indicated that the proposed 4L approach consistently led to the highest level of accuracy at a given number of employed atlases in both adult and geriatric populations. In addition, the proposed two methods (4L and LV) can reduce 20 times computational time compared with the stereotypical mutual information-based method. Our pre-selection strategy would provide better segmentation performance in terms of both accuracy and efficiency. The proposed atlas pre-selection will be further implemented into our online automatic brain image segmentation system (www.mricloud.org).
| S-EPMC6063392 | biostudies-literature
Project description:Existing intracortical brain computer interfaces (iBCIs) transform neural activity into control signals capable of restoring movement to persons with paralysis. However, the accuracy of the 'decoder' at the heart of the iBCI typically degrades over time due to turnover of recorded neurons. To compensate, decoders can be recalibrated, but this requires the user to spend extra time and effort to provide the necessary data, then learn the new dynamics. As the recorded neurons change, one can think of the underlying movement intent signal being expressed in changing coordinates. If a mapping can be computed between the different coordinate systems, it may be possible to stabilize the original decoder's mapping from brain to behavior without recalibration. We previously proposed a method based on Generalized Adversarial Networks (GANs), called 'Adversarial Domain Adaptation Network' (ADAN), which aligns the distributions of latent signals within underlying low-dimensional neural manifolds. However, we tested ADAN on only a very limited dataset. Here we propose a method based on Cycle-Consistent Adversarial Networks (Cycle-GAN), which aligns the distributions of the full-dimensional neural recordings. We tested both Cycle-GAN and ADAN on data from multiple monkeys and behaviors and compared them to a third, quite different method based on Procrustes alignment of axes provided by Factor Analysis. All three methods are unsupervised and require little data, making them practical in real life. Overall, Cycle-GAN had the best performance and was easier to train and more robust than ADAN, making it ideal for stabilizing iBCI systems over time.
| S-EPMC10446822 | biostudies-literature
Project description:PurposeIn this work, we addressed fully automatic determination of tumor functional uptake from positron emission tomography (PET) images without relying on other image modalities or additional prior constraints, in the context of multicenter images with heterogeneous characteristics.MethodsIn cervical cancer, an additional challenge is the location of the tumor uptake near or even stuck to the bladder. PET datasets of 232 patients from five institutions were exploited. To avoid unreliable manual delineations, the ground truth was generated with a semi-automated approach: a volume containing the tumor and excluding the bladder was first manually determined, then a well-validated, semi-automated approach relying on the Fuzzy locally Adaptive Bayesian (FLAB) algorithm was applied to generate the ground truth. Our model built on the U-Net architecture incorporates residual blocks with concurrent spatial squeeze and excitation modules, as well as learnable non-linear downsampling and upsampling blocks. Experiments relied on cross-validation (four institutions for training and validation, and the fifth for testing).ResultsThe model achieved good Dice similarity coefficient (DSC) with little variability across institutions (0.80 ± 0.03), with higher recall (0.90 ± 0.05) than precision (0.75 ± 0.05) and improved results over the standard U-Net (DSC 0.77 ± 0.05, recall 0.87 ± 0.02, precision 0.74 ± 0.08). Both vastly outperformed a fixed threshold at 40% of SUVmax (DSC 0.33 ± 0.15, recall 0.52 ± 0.17, precision 0.30 ± 0.16). In all cases, the model could determine the tumor uptake without including the bladder. Neither shape priors nor anatomical information was required to achieve efficient training.ConclusionThe proposed method could facilitate the deployment of a fully automated radiomics pipeline in such a challenging multicenter context.
| S-EPMC8440243 | biostudies-literature
Project description:ObjectiveTo test the relationship between external environments, organizational characteristics, and technical efficiency in federally qualified health centers (FQHCs). We tested the relationship between grant revenue and technical efficiency in FQHCs.Data sources/study designSecondary data were collected in each year from the Uniform Data System (UDS) on 644 eligible U.S.-based FQHCs between 2005 and 2007. The study employs a retrospective longitudinal cohort design with instrumental variables.Principal findingsIncreased grant revenues did not increase the probability that a health center would be on the efficiency frontier. However, increased grant revenues had a negative association with technical efficiency for health centers that were not fully efficient.ConclusionIf all health centers were operating efficiently, anywhere from 39 to 45 million patient encounters could have been delivered instead of the actual total of 29 million in 2007. Policy makers should consider tying grant revenues to performance indicators, and future work is needed to understand the mechanisms through which diseconomies of scale are present in FQHCs.
| S-EPMC3976192 | biostudies-literature
Project description:Prior research tends to propose and examine the negative relationship between market segmentation and energy efficiency. Does market segmentation necessarily impair energy efficiency? Considering the critical role that Chinaese government play in managing erergy efficiency, we propose a non-linear relationship between market segmentation and energy efficiency. Using data of 30 provinces in Mainland China during 2000 to 2017, we find an inverse U-shaped relationship between market segmentation and energy efficiency. Our findings remain robust after controlling endogeneity issues. Therefore, a moderate level of market segmentation is acceptable and beneficial for long-term improvement of energy efficiency in emerging economies.
| S-EPMC7241797 | biostudies-literature
Project description:The transport layer security (TLS) protocol is widely adopted by apps as well as malware. With the geometric growth of TLS traffic, accurate and efficient detection of malicious TLS flows is becoming an imperative. However, current studies focus on either detection accuracy or detection efficiency, and few studies take into account both indicators. In this paper, we propose a two-layer detection framework composed of a filtering model (FM) and a malware family classification model (MFCM). In the first layer, a new set of TLS handshake features is presented to train the FM, which is devised to filter out a majority of benign TLS flows. For identifying malware families, both TLS handshake features and statistical features are applied to construct the MFCM in the second layer. Comprehensive experiments are conducted to substantiate the high accuracy and efficiency of the proposed two-layer framework. A total of 96.32% of benign TLS flows can be filtered out by the FM with few malicious TLS flows being discarded provided the threshold of the FM is set to 0.01. Moreover, a multiclassifier is selected to construct the MFCM to provide better performance than a set of binary classifiers under the same feature set. In addition, when the ratio of benign and malicious TLS flows is set to 10:1, the detection efficiency of the two-layer framework is 188% faster than that of the single-layer framework, while the average detection accuracy reaches 99.45%.
| S-EPMC7202608 | biostudies-literature
Project description:Proper functioning of biological cells requires that the process of protein expression be carried out with high efficiency and fidelity. Given an amino-acid sequence of a protein, multiple degrees of freedom still remain that may allow evolution to tune efficiency and fidelity for each gene under various conditions and cell types. Particularly, the redundancy of the genetic code allows the choice between alternative codons for the same amino acid, which, although 'synonymous,' may exert dramatic effects on the process of translation. Here we review modern developments in genomics and systems biology that have revolutionized our understanding of the multiple means by which translation is regulated. We suggest new means to model the process of translation in a richer framework that will incorporate information about gene sequences, the tRNA pool of the organism and the thermodynamic stability of the mRNA transcripts. A practical demonstration of a better understanding of the process would be a more accurate prediction of the proteome, given the transcriptome at a diversity of biological conditions.
| S-EPMC3101949 | biostudies-other