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"Yu, L"
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Handbook of phonological theory
In a series of essays on topics as varied as underspecification theory, prosodic morphology, and syllable structure, 38 leading phonologists offer a critical survey of the leading and guiding ideas that lie behind the research in this active area of linguistic research.
Book
Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares
Gene-expression deconvolution is used to quantify different types of cells in a mixed population. It provides a highly promising solution to rapidly characterize the tumor-infiltrating immune landscape and identify cold cancers. However, a major challenge is that gene-expression data are frequently contaminated by many outliers that decrease the estimation accuracy. Thus, it is imperative to develop a robust deconvolution method that automatically decontaminates data by reliably detecting and removing outliers. We developed a new machine learning tool, Fast And Robust DEconvolution of Expression Profiles (FARDEEP), to enumerate immune cell subsets from whole tumor tissue samples. To reduce noise in the tumor gene expression datasets, FARDEEP utilizes an adaptive least trimmed square to automatically detect and remove outliers before estimating the cell compositions. We show that FARDEEP is less susceptible to outliers and returns a better estimation of coefficients than the existing methods with both numerical simulations and real datasets. FARDEEP provides an estimate related to the absolute quantity of each immune cell subset in addition to relative percentages. Hence, FARDEEP represents a novel robust algorithm to complement the existing toolkit for the characterization of tissue-infiltrating immune cell landscape. The source code for FARDEEP is implemented in R and available for download at https://github.com/YuningHao/FARDEEP.git.
Journal Article
Hadron multiplicity fluctuations in perturbative QCD
A
bstract
We examine hadron multiplicity fluctuations in hard processes and confront analytic QCD predictions with the pattern of multiplicity fluctuations observed in
e
+
e
−
annihilation and high-
p
t
jets produced in
pp
collisions at the LHC. Special emphasis is placed on high-multiplicity fluctuations in jets. Selecting events with hadronic multiplicity exceeding the average value by a factor of 3 or more in various processes has been a source of conundrums for many years. We discuss two recent high-multiplicity puzzles and attempt to reveal their common origin.
Journal Article
QCD-inspired description of multiplicity distributions in jets
A
bstract
We suggest a universal QCD-motivated expression for the Polyakov-KNO multiplicity distributions of hadrons in jets and compare it with data from
e
+
e
−
annihilation experiments. The moments and overall shape of the distributions in full events and quark and gluon jets, over a range of energies, are described with reasonable quantitative precision. In particular, the scaling violation predicted by QCD is seen clearly in the moments and high-multiplicity fluctuations.
Journal Article
Transcriptional and posttranscriptional regulation of HOXA13 by lncRNA HOTTIP facilitates tumorigenesis and metastasis in esophageal squamous carcinoma cells
The long non-coding RNA, HOTTIP, has an important role in tumorigenesis. It is known that HOTTIP regulates HOX gene family; however, its regulatory mechanism in esophageal squamous cell carcinoma (ESCC) remains elusive. In this study, we investigated the role of HOTTIP in ESCC and observed that HOTTIP/HOXA13 was upregulated in ESCC and promoted cell proliferation and metastasis
in vivo
and
in vitro
. Interestingly, harboring a miR-30b-binding site, HOTTIP as a molecular sponge mainly regulated miR-30b level in the nucleus and modulated the repression of HOXA13 mediated by miR-30b in the cytoplasm, resulting in the positive HOTTIP/HOXA13 correlation. In addition, HOTTIP upregulated snail1 by competitively binding miR-30b, subsequently promoting epithelial–mesenchymal transition (EMT) and invasion. HOTTIP directly bound the adaptor protein WDR5 and drove histone H3 lysine 4 trimethylation and HOXA13 gene transcription in ESCC cells. In conclusion, our findings indicated that HOTTIP modulated HOXA13 at both the transcriptional and posttranscriptional levels in ESCC cells and HOTTIP–miR-30b–HOXA13 axis may serve as potential diagnostic markers or drug targets for ESCC therapies.
Journal Article
Cross-site transportability of an explainable artificial intelligence model for acute kidney injury prediction
Artificial intelligence (AI) has demonstrated promise in predicting acute kidney injury (AKI), however, clinical adoption of these models requires interpretability and transportability. Non-interoperable data across hospitals is a major barrier to model transportability. Here, we leverage the US PCORnet platform to develop an AKI prediction model and assess its transportability across six independent health systems. Our work demonstrates that cross-site performance deterioration is likely and reveals heterogeneity of risk factors across populations to be the cause. Therefore, no matter how accurate an AI model is trained at the source hospital, whether it can be adopted at target hospitals is an unanswered question. To fill the research gap, we derive a method to predict the transportability of AI models which can accelerate the adaptation process of external AI models in hospitals.
Artificial intelligence (AI) has demonstrated promise in predicting acutekidney injury (AKI), however, clinical adoption of these models requires interpretability and transportability across sites. Here, the authors develop an AKI prediction model and a measure for model transportability across six independent health systems.
Journal Article
Neural Manifestations of Implicit Self-Esteem: An ERP Study
Behavioral research has established that humans implicitly tend to hold a positive view toward themselves. In this study, we employed the event-related potential (ERP) technique to explore neural manifestations of positive implicit self-esteem using the Go/Nogo association task (GNAT). Participants generated a response (Go) or withheld a response (Nogo) to self or others words and good or bad attributes. Behavioral data showed that participants responded faster to the self paired with good than the self paired with bad, whereas the opposite proved true for others, reflecting the positive nature of implicit self-esteem. ERP results showed an augmented N200 over the frontal areas in Nogo responses relative to Go responses. Moreover, the positive implicit self-positivity bias delayed the onset time of the N200 wave difference between Nogo and Go trials, suggesting that positive implicit self-esteem is manifested on neural activity about 270 ms after the presentation of self-relevant stimuli. These findings provide neural evidence for the positivity and automaticity of implicit self-esteem.
Journal Article
Ultra-fast proteomics with Scanning SWATH
Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min
–1
) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5–5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.
Scanning SWATH increases the speed and selectivity of proteomics.
Journal Article