Nuclear export of circular RNA.

Circular RNAs (circRNAs), which are increasingly being implicated in a variety of functions in normal and cancerous cells1-5, are formed by back-splicing of precursor mRNAs in the nucleus6-10. circRNAs are predominantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here we identify a pathway that is specific for the nuclear export of circular RNA. This pathway requires Ran-GTP, exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter CRM1 selectively increases the nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Depletion or knockout of exportin-2 specifically inhibits nuclear export of circRNA. Analysis of nuclear circRNA-binding proteins reveals that interaction between IGF2BP1 and circRNA is enhanced by Ran-GTP. The formation of circRNA export complexes in the nucleus is promoted by Ran-GTP through its interactions with exportin-2, circRNA and IGF2BP1. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Ran-GTP and exportin-2 to export circRNAs in a mechanism that is analogous to protein export, rather than mRNA export.

Liquid-liquid phase separation in innate immunity.

Intrinsic and innate immune responses are essential lines of defense in the body's constant surveillance of pathogens. The discovery of liquid-liquid phase separation (LLPS) as a key regulator of this primal response to infection brings an updated perspective to our understanding of cellular defense mechanisms. Here, we review the emerging multifaceted role of LLPS in diverse aspects of mammalian innate immunity, including DNA and RNA sensing and inflammasome activity. We discuss the intricate regulation of LLPS by post-translational modifications (PTMs), and the subversive tactics used by viruses to antagonize LLPS. This Review, therefore, underscores the significance of LLPS as a regulatory node that offers rapid and plastic control over host immune signaling, representing a promising target for future therapeutic strategies.

ESRP1 controls biogenesis and function of a large abundant multiexon circRNA.

While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2-27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal transition (EMT) and whose formation depends on the epithelial splicing regulator ESRP1. CircDOCK1(2-27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis and CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2-27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 may modify the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.

The viral packaging motor potentiates Kaposi's sarcoma-associated herpesvirus gene expression late in infection.

ß- and γ-herpesviruses transcribe their late genes in a manner distinct from host transcription. This process is directed by a complex of viral transcriptional activator proteins that hijack cellular RNA polymerase II and an unknown set of additional factors. We employed proximity labeling coupled with mass spectrometry, followed by CRISPR and siRNA screening to identify proteins functionally associated with the Kaposi's sarcoma-associated herpesvirus (KSHV) late gene transcriptional complex. These data revealed that the catalytic subunit of the viral DNA packaging motor, ORF29, is both dynamically associated with the viral transcriptional activator complex and potentiates gene expression late in infection. Through genetic mutation and deletion of ORF29, we establish that its catalytic activity potentiates viral transcription and is required for robust accumulation of essential late proteins during infection. Thus, we propose an expanded role for ORF29 that encompasses its established function in viral packaging and its newly discovered contributions to viral transcription and late gene expression in KSHV.

Chang'E-4 initial spectroscopic identification of lunar far-side mantle-derived materials.

Over 60 years of spacecraft exploration has revealed that the Earth's Moon is characterized by a lunar crust1 dominated by the mineral plagioclase, overlying a more mafic (richer in iron and magnesium) mantle of uncertain composition. Both crust and mantle formed during the earliest stages of lunar evolution when late-stage accretional energy caused a molten rock (magma) ocean, flotation of the light plagioclase, sinking of the denser iron-rich minerals, such as olivine and pyroxene, and eventually solidification2. Very large impact craters can potentially penetrate through the crust and sample the lunar mantle. The largest of these craters is the approximately 2,500-kilometre-diameter South Pole-Aitken (SPA) basin3 on the lunar far side. Evidence obtained from orbiting spacecraft shows that the floor of the SPA basin is rich in mafic minerals4, but their mantle origin is controversial and their in situ geologic settings are poorly known. China's Chang'E-4 lunar far-side lander recently touched down in the Von Kármán crater5,6 to explore the floor of the huge SPA basin and deployed its rover, Yutu-2. Here we report on the initial spectral observations of the Visible and Near Infrared Spectrometer (VNIS)7 onboard Yutu-2, which we interpret to represent the presence of low-calcium (ortho)pyroxene and olivine, materials that may originate from the lunar mantle. Geological context6 suggests that these materials were excavated from below the SPA floor by the nearby 72-km-diameter Finsen impact crater event, and transported to the landing site. Continued exploration by Yutu-2 will target these materials on the floor of the Von Kármán crater to understand their geologic context, origin and abundance, and to assess the possibility of sample-return scenarios.

IFI16 phase separation via multi-phosphorylation drives innate immune signaling.

The interferon inducible protein 16 (IFI16) is a prominent sensor of nuclear pathogenic DNA, initiating innate immune signaling and suppressing viral transcription. However, little is known about mechanisms that initiate IFI16 antiviral functions or its regulation within the host DNA-filled nucleus. Here, we provide in vitro and in vivo evidence to establish that IFI16 undergoes liquid-liquid phase separation (LLPS) nucleated by DNA. IFI16 binding to viral DNA initiates LLPS and induction of cytokines during herpes simplex virus type 1 (HSV-1) infection. Multiple phosphorylation sites within an intrinsically disordered region (IDR) function combinatorially to activate IFI16 LLPS, facilitating filamentation. Regulated by CDK2 and GSK3ß, IDR phosphorylation provides a toggle between active and inactive IFI16 and the decoupling of IFI16-mediated cytokine expression from repression of viral transcription. These findings show how IFI16 switch-like phase transitions are achieved with temporal resolution for immune signaling and, more broadly, the multi-layered regulation of nuclear DNA sensors.

On the rules of engagement for microRNAs targeting protein coding regions.

MiRNAs post-transcriptionally repress gene expression by binding to mRNA 3'UTRs, but the extent to which they act through protein coding regions (CDS regions) is less well established. MiRNA interaction studies show a substantial proportion of binding occurs in CDS regions, however sequencing studies show much weaker effects on mRNA levels than from 3'UTR interactions, presumably due to competition from the translating ribosome. Consequently, most target prediction algorithms consider only 3'UTR interactions. However, the consequences of CDS interactions may have been underestimated, with the reporting of a novel mode of miRNA-CDS interaction requiring base pairing of the miRNA 3' end, but not the canonical seed site, leading to repression of translation with little effect on mRNA turnover. Using extensive reporter, western blotting and bioinformatic analyses, we confirm that miRNAs can indeed suppress genes through CDS-interaction in special circumstances. However, in contrast to that previously reported, we find repression requires extensive base-pairing, including of the canonical seed, but does not strictly require base pairing of the 3' miRNA terminus and is mediated through reducing mRNA levels. We conclude that suppression of endogenous genes can occur through miRNAs binding to CDS, but the requirement for extensive base-pairing likely limits the regulatory impacts to modest effects on a small subset of targets.

TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization.

Deciphering the cell-type composition in the tumor immune microenvironment (TIME) can significantly increase the efficacy of cancer treatment and improve the prognosis of cancer. Such a task has benefited from microarrays and RNA sequencing technologies, which have been widely adopted in cancer studies, resulting in extensive expression profiles with clinical phenotypes across multiple cancers. Current state-of-the-art tools can infer cell-type composition from bulk expression profiles, providing the possibility of investigating the inter-heterogeneity and intra-heterogeneity of TIME across cancer types. Much can be gained from these tools in conjunction with a well-curated database of TIME cell-type composition data, accompanied by the corresponding clinical information. However, currently available databases fall short in data volume, multi-platform dataset integration, and tool integration. In this work, we introduce TIMEDB (https://timedb.deepomics.org), an online database for human tumor immune microenvironment cell-type composition estimated from bulk expression profiles. TIMEDB stores manually curated expression profiles, cell-type composition profiles, and the corresponding clinical information of a total of 39,706 samples from 546 datasets across 43 cancer types. TIMEDB comes readily equipped with online tools for automatic analysis and interactive visualization, and aims to serve the community as a convenient tool for investigating the human tumor microenvironment.

Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis.

Regulatory T (Treg) cells are essential for maintenance of immune homeostasis. Here we found that hydrogen sulfide (H2S) was required for Foxp3(+) Treg cell differentiation and function and that H2S deficiency led to systemic autoimmune disease. H2S maintained expression of methylcytosine dioxygenases Tet1 and Tet2 by sulfhydrating nuclear transcription factor Y subunit beta (NFYB) to facilitate its binding to Tet1 and Tet2 promoters. Transforming growth factor-ß (TGF-ß)-activated Smad3 and interleukin-2 (IL-2)-activated Stat5 facilitated Tet1 and Tet2 binding to Foxp3. Tet1 and Tet2 catalyzed conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in Foxp3 to establish a Treg-cell-specific hypomethylation pattern and stable Foxp3 expression. Consequently, Tet1 and Tet2 deletion led to Foxp3 hypermethylation, impaired Treg cell differentiation and function, and autoimmune disease. Thus, H2S promotes Tet1 and Tet2 expression, which are recruited to Foxp3 by TGF-ß and IL-2 signaling to maintain Foxp3 demethylation and Treg-cell-associated immune homeostasis.

Bifurcation analysis and control of improved traffic flow model considering the effect of strong winds.

In recent years, the problem of traffic congestion has become increasingly serious, and research on traffic system control has become a new hotspot. Studying the bifurcation characteristics of traffic flow systems and designing control schemes for unstable support points can alleviate traffic congestion from a new perspective. This article improves the full speed differential model considering strong wind models from the perspective of bifurcation control to adjust traffic flow. This article theoretically proves the existence conditions of Hopf bifurcation and saddle node bifurcation in the model and finds the stability mutation point of the transportation system stability. A nonlinear system feedback controller was designed for unstable bifurcation points using Chebyshev polynomial approximation and random feedback control methods. Without changing the system equilibrium point, the advance, delay, and elimination of Hopf bifurcation were achieved, and the abrupt behavior of the transportation system was controlled, thereby alleviating traffic congestion. This article explains the changes in the stability of complex transportation systems from the perspective of bifurcation analysis, which can better capture the characteristics of traffic flow. By adjusting the control parameters in the feedback controller, the influence of boundary conditions on the stability of the transportation system is fully described, and the influence of unstable focal points and saddle points on the system is suppressed, thereby slowing down the traffic flow. In addition, unstable bifurcation points can be eliminated, and the Hopf bifurcation can be controlled to advance, delay, and disappear, thereby achieving control over the stable behavior of the transportation system. This helps alleviate traffic congestion and also helps describe actual traffic phenomena.

Kinetics of hydrogen absorption/desorption in the Zr-2.5Nb alloy.

The Zr-2.5Nb alloy is a typical pressure tube material in heavy water nuclear reactors, and an increase of hydrogen isotope content in the alloy during service can pose major safety risks; hot vacuum extraction-mass spectrometry is an efficient method for evaluating hydrogen isotope concentrations in the Zr-2.5Nb alloy. This work investigates the kinetics and thermodynamic properties of deuterium (D) absorption and desorption of the Zr-2.5Nb alloy using the constant volume adsorption method and the hot vacuum extraction method. In addition to the previously reported volume contraction model, it was observed that at 600 °C and above, the reaction between D2 and Zr-2.5Nb is dominated by diffusion, while the reaction is predominantly influenced by surface adsorption and dissociation below 600 °C. Phase transition sequence of Zr-2.5Nb deuterides during non-isothermal desorption was established using quantitatively calibrated thermal desorption spectra combined with the phase transition process of deuteride decomposition. These results can provide important references for optimizing the process parameters of the hot vacuum extraction-mass spectrometry method.

Biomechanical effects of clear aligner with different shape design at extraction space area during anterior teeth retraction.

OBJECTIVE: This study aimed to investigate the biomechanical effects of clear aligner (CA) with different shape designs at extraction space (CAES) area during space closing. MATERIALS AND METHODS: A finite-element method (FEM) model of mandibular dentition, periodontal ligaments, attachments, and corresponding CA was established. The connecting rod design of CAES was modelled for the control group. Eight test groups with different heights of CAES from -4 mm to +4 mm were designed. Tooth displacement tendencies were calculated. The maximum principal stress in PDLs, teeth, and CAs was analysed. Both global coordinate system and local coordinate system were also used to evaluate individual tooth movements. RESULTS: Across all groups, stresses concentrated on the lingual outer surface of CAESs. For the lowered CAES groups, both the stress value and the stress distribution area at CAESs were increased. The lowered CAES groups showed reduced movement in anterior teeth and less tipping tendency of the canines. CONCLUSION: The shape of CAES has a biomechanical impact on anterior teeth movement and should be considered in aligner design. The results suggest that increasing the height of CAES can enhance anterior teeth retraction, while lowered CAES may facilitate controlled root movement. Changes in the shape of CAES represent a potential direction for biomechanical improvement of clear aligner in extraction cases and are worth exploring.

Inhibition of Th17 cell differentiation by aerobic exercise improves vasodilatation in diabetic mice.

BACKGROUND: Aortic endothelial diastolic dysfunction is an early complication of diabetes and the abnormal differentiation of Th17 cells is involved in the development of diabetes. However, the exact role of exercise on regulating the Th17 cells differentiation and the underlying molecular mechanisms remain to be elucidated in diabetic mice. METHODS: db/db and db/m+ mice were randomly divided into exercise and sedentary groups. Mice in exercise group were exercised daily, 6 days/week, for 6 weeks and mice in sedentary groups were placed on a nonmoving treadmill for 6 weeks. Vascular endothelial function was measured via wire myograph and the frequencies of Th17 from peripheral blood in mice were assessed via flow cytometry. RESULTS: Our data showed that exercise improved insulin resistance and aortic endothelial diastolic function in db/db mice. In addition, the proportion of Th17 cells and IL-17A level in peripheral blood of db/db mice were significantly increased, and exercise could promote Th17 cell differentiation and reduce IL-17A level. More importantly, STAT3 or ROR-γt inhibitors could promote Th17 cell differentiation in db/db mice, while exercise significantly down-regulated p-STAT3/ROR-γt signaling in db/db mice, suggesting that exercise regulated Th17 differentiation through STAT3/ROR-γt signaling. CONCLUSIONS: This study demonstrated that exercise improved vascular endothelial function in diabetic mice via reducing Th17 cell differentiation through p-STAT3/ROR-γt pathway, suggesting exercise may be an important non-pharmacological intervention strategy for the treatment of diabetes-related vascular complications.

Kaposi's sarcoma herpesvirus is associated with osteosarcoma in Xinjiang populations.

Osteosarcoma is the most common malignant tumor of bone predominately affecting adolescents and young adults. Based on animal studies, a viral etiology of osteosarcoma was proposed more than a half-century ago, but no viral association with human osteosarcoma has been found. The Uyghur ethnic population in Xinjiang, China, has an unusually high prevalence of Kaposi's sarcoma-associated herpesvirus (KSHV) infection and elevated incidence of osteosarcoma. In the current study, we explored the possible association of KSHV infection and osteosarcoma occurrence. Our seroepidemiological study revealed that KSHV prevalence was significantly elevated in Uyghur osteosarcoma patients versus the general Uyghur population (OR, 10.23; 95%CI, 4.25, 18.89). The KSHV DNA genome and viral latent nuclear antigen LANA were detected in most osteosarcoma tumor cells. Gene expression profiling analysis showed that KSHV-positive osteosarcoma represents a distinct subtype of osteosarcomas with viral gene-activated signaling pathways important for osteosarcoma development. We conclude that KSHV infection is a risk factor for osteosarcoma, and KSHV is associated with some osteosarcomas, representing a newly identified viral-associated endemic cancer.

Delta/Jagged-mediated Notch signaling induces the differentiation of agr2-positive epidermal mucous cells in zebrafish embryos.

Teleosts live in aquatic habitats, where they encounter ionic and acid-base fluctuations as well as infectious pathogens. To protect from these external challenges, the teleost epidermis is composed of living cells, including keratinocytes and ionocytes that maintain body fluid ionic homeostasis, and mucous cells that secret mucus. While ionocyte progenitors are known to be specified by Delta-Notch-mediated lateral inhibition during late gastrulation and early segmentation, it remains unclear how epidermal mucous cells (EMCs) are differentiated and maintained. Here, we show that Delta/Jagged-mediated activation of Notch signaling induces the differentiation of agr2-positive (agr2+) EMCs in zebrafish embryos during segmentation. We demonstrated that agr2+ EMCs contain cytoplasmic secretory granules and express muc5.1 and muc5.2. Reductions in agr2+ EMC number were observed in mib mutants and notch3 MOs-injected notch1a mutants, while increases in agr2+ cell number were detected in notch1a- and X-Su(H)/ANK-overexpressing embryos. Treatment with γ-secretase inhibitors further revealed that Notch signaling is required during bud to 15 hpf for the differentiation of agr2+ EMCs. Increased agr2+ EMC numbers were also observed in jag1a-, jag1b-, jag2a- and dlc-overexpressing, but not jag2b-overexpressing embryos. Meanwhile, reductions in agr2+ EMC numbers were detected in jag1a morphants, jag1b mutants, jag2a mutants and dlc morphants, but not jag2b mutants. Reduced numbers of pvalb8-positive epidermal cells were also observed in mib or jag2a mutants and jag1a or jag1b morphants, while increased pvalb8-positive epidermal cell numbers were detected in notch1a-overexpressing, but not dlc-overexpressing embryos. BrdU labeling further revealed that the agr2+ EMC population is maintained by proliferation. Cell lineage experiments showed that agr2+ EMCs are derived from the same ectodermal precursors as keratinocytes or ionocytes. Together, our results indicate that specification of agr2+ EMCs in zebrafish embryos is induced by DeltaC/Jagged-dependent activation of Notch1a/3 signaling, and the cell population is maintained by proliferation.

Growth Evaluation After Costochondral Graft Combined With Functional Appliance in Children With Temporomandibular Joint Ankylosis.

The treatment of temporomandibular joint (TMJ) ankylosis in children is a great challenge for surgeons. Costochondral graft (CCG) is a common method of reconstructing the TMJ in children. However, the growth pattern of CCG is unpredictable. In this study, we introduced a surgical-orthodontic approach and evaluated the growth results of the mandible and maxilla in children with TMJ ankylosis through 3-dimensional computed tomography measurements. A prospective cohort study was conducted on child patients diagnosed as having TMJ ankylosis between September 1, 2018 and June 1, 2020. Computer-aided virtual mandibular position guided the CCG, and removable functional appliance was used after surgery. The maximal incisal opening (MIO), the maxilla height, and the length of mandibular ramus were determined. Paired t test was performed to analyze the differences among various stages. Six patients (3 females, 3 males; aged 6-9 y) were included in this study. MIO was 12.4 mm before surgery and improved to 36.8 mm after 42.8 months' follow-up. Mandible length increased by 5.1 mm in the affected side and by 5.3 mm in the unaffected side, without significant difference. The affected maxilla height increased by 6.7 mm, which was more than 5.0 mm in the unaffected side. In conclusion, continued growth of mandible and maxilla can be achieved through CCG combined with functional appliance treatment for children TMJ ankylosis.

Mandibular cortical bone remodeling characteristics in patients with extraction: A cone-beam computed tomography study.

INTRODUCTION: This study evaluated the labial and lingual cortical bone remodeling characteristics of mandibular central incisors after retraction, which remain controversial among orthodontists. METHODS: Cortical bone remodeling and central incisor movement of 33 patients (aged 23.64 ± 4.30 years) who underwent mandibular first premolar extraction and incisor retraction at the crestal (S1), midroot (S2), and apical (S3) levels were analyzed using superimposed cone-beam computed tomography images on the basis of voxel-based registration of the mandibular stable region. Multivariate linear regression was used to explore the relationships between labial bone remodeling/tooth movement (BT) ratios and factors such as the ANB angle, mandibular plane angle (Mp-SN), and incisor movement patterns. The patients were divided into 4 groups according to the lingual cortical bone remodeling condition and the relationship between posttreatment incisor roots and the original lingual cortical bone border. At the 3 levels (S1, S2, and S3), the classifications of cortical bone remodeling of the mandibular incisors were calculated; t tests were used to compare the amount of labial and lingual bone remodeling, BT ratios, and lingual bone remodeling/root over the original border (BRo) ratios. RESULTS: The mean labial BT ratios at all 3 levels were close to 1. Multivariate linear regression indicated that the tooth movement pattern negatively correlated with the BT ratio at the S2 and S3 levels (P <0.05). Lingual bone apposition occurs when the root penetrates the original lingual cortical bone border in most patients. BRo ratios can more accurately reflect the inherent remodeling ability of the lingual cortical bone than BT ratios. The mean lingual BRo ratios were (1) S1 level: mandibular left central incisor (T31), 0.87 ± 0.25 and mandibular right incisor (T41), 0.86 ± 0.25; (2) S2 level: T31, 0.81 ± 0.12 and T41, 0.80 ± 0.22; and (3) S3 level: T31, 0.76 ± 0.20 and T41, 0.83 ± 0.26. There was no significant difference between labial BT ratios and lingual BRo ratios at the S2 and S3 levels. CONCLUSIONS: The amount of labial cortical bone resorption caused by mandibular incisor retraction showed varied relationships with the amount of tooth movement. Bodily retraction may decrease the labial BT ratios at the S2 and S3 levels. Active lingual cortical bone apposition occurred when the roots penetrated the original lingual border and exhibited strong remodeling ability.

[Preliminary evaluation of chin symmetry with three dimentional soft tissue spatial angle wireframe template].

OBJECTIVE: To develop an efficient and robust method based on three dimensional facial landmarks for evaluating chin region asymmetry at the soft tissue level and to compare it with the traditional mirror-overlap analysis method in order to test its availability. METHODS: Standard symmetrical face was used for mental tubercle coordinate transformation so as to filter soft tissue three dimensional spatial angle and construct corresponding three dimensional spatial angle wireframe template. Ten patients aged 12-32 years with clinical chin region asymmetry diagnosis at the Department of Orthodontics of Peking University Hospital of Stomatology from November 2020 to November 2021 were randomly selected. Three dimensional soft tissue face scan data of the patients were collected by three dimensional face scanner and the landmark points were automatically determined by the Meshmonk non-rigid registration algorithm program, and in this way, the asymmetric three dimensional spatial angle wireframe template and corresponding spatial angle parameters were generated. Mirror-overlap analysis of face scan data was also performed in Geomagic Studio 2015 software and deviation color maps were generated. This study took mirror-overlap analysis as the gold standard method, the response rate of chin region asymmetry was eva-luated by the outcomes of the mirror-overlap analysis and three dimensional spatial angle wireframe template analysis. RESULTS: Nine three dimensional spatial angle indicators were selected through coordinate transformation, and the response rate was calculated using mirror-overlap analysis as the gold standard method. Among these ten selected patients, the response rate of the total chin region asymmetry was 90% (9/10). Using the deviation value of mirror-overlap analysis as a reference, the response rate of chin region asymmetry in the X dimension was 86%, the response rate of chin region asymmetry in the Y dimension was 89%, and the response rate of chin region asymmetry in the Z dimension was 100%. CONCLUSION: The three dimensional soft tissue spatial angle wireframe template proposed in this study has some feasibility in evaluating chin region asymmetry at the soft tissue level, and its ability to recognize asymmetry separately in the three dimensional direction is better than the mirror-overlap analysis method, and the indicators recognition rate still needs to be further improved.

Single-timepoint low-dimensional characterization and classification of acute versus chronic multiple sclerosis lesions using machine learning.

Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease characterized by the appearance of focal lesions across the central nervous system. The discrimination of acute from chronic MS lesions may yield novel biomarkers of inflammatory disease activity which may support patient management in the clinical setting and provide endpoints in clinical trials. On a single timepoint and in the absence of a prior reference scan, existing methods for acute lesion detection rely on the segmentation of hyperintense foci on post-gadolinium T1-weighted magnetic resonance imaging (MRI), which may underestimate recent acute lesion activity. In this paper, we aim to improve the sensitivity of acute MS lesion detection in the single-timepoint setting, by developing a novel machine learning approach for the automatic detection of acute MS lesions, using single-timepoint conventional non-contrast T1- and T2-weighted brain MRI. The MRI input data are supplemented via the use of a convolutional neural network generating "lesion-free" reconstructions from original "lesion-present" scans using image inpainting. A multi-objective statistical ranking module evaluates the relevance of textural radiomic features from the core and periphery of lesion sites, compared within "lesion-free" versus "lesion-present" image pairs. Then, an ensemble classifier is optimized through a recursive loop seeking consensus both in the feature space (via a greedy feature-pruning approach) and in the classifier space (via model selection repeated after each pruning operation). This leads to the identification of a compact textural signature characterizing lesion phenotype. On the patch-level task of acute versus chronic MS lesion classification, our method achieves a balanced accuracy in the range of 74.3-74.6% on fully external validation cohorts.