Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation.

BACKGROUND: The integration of single-cell RNA sequencing data from multiple experimental batches and diverse biological conditions holds significant importance in the study of cellular heterogeneity. RESULTS: To expedite the exploration of systematic disparities under various biological contexts, we propose a scRNA-seq integration method called scDisco, which involves a domain-adaptive decoupling representation learning strategy for the integration of dissimilar single-cell RNA data. It constructs a condition-specific domain-adaptive network founded on variational autoencoders. scDisco not only effectively reduces batch effects but also successfully disentangles biological effects and condition-specific effects, and further augmenting condition-specific representations through the utilization of condition-specific Domain-Specific Batch Normalization layers. This enhancement enables the identification of genes specific to particular conditions. The effectiveness and robustness of scDisco as an integration method were analyzed using both simulated and real datasets, and the results demonstrate that scDisco can yield high-quality visualizations and quantitative outcomes. Furthermore, scDisco has been validated using real datasets, affirming its proficiency in cell clustering quality, retaining batch-specific cell types and identifying condition-specific genes. CONCLUSION: scDisco is an effective integration method based on variational autoencoders, which improves analytical tasks of reducing batch effects, cell clustering, retaining batch-specific cell types and identifying condition-specific genes.

scAce: an adaptive embedding and clustering method for single-cell gene expression data.

MOTIVATION: Since the development of single-cell RNA sequencing (scRNA-seq) technologies, clustering analysis of single-cell gene expression data has been an essential tool for distinguishing cell types and identifying novel cell types. Even though many methods have been available for scRNA-seq clustering analysis, the majority of them are constrained by the requirement on predetermined cluster numbers or the dependence on selected initial cluster assignment. RESULTS: In this article, we propose an adaptive embedding and clustering method named scAce, which constructs a variational autoencoder to simultaneously learn cell embeddings and cluster assignments. In the scAce method, we develop an adaptive cluster merging approach which achieves improved clustering results without the need to estimate the number of clusters in advance. In addition, scAce provides an option to perform clustering enhancement, which can update and enhance cluster assignments based on previous clustering results from other methods. Based on computational analysis of both simulated and real datasets, we demonstrate that scAce outperforms state-of-the-art clustering methods for scRNA-seq data, and achieves better clustering accuracy and robustness. AVAILABILITY AND IMPLEMENTATION: The scAce package is implemented in python 3.8 and is freely available from https://github.com/sldyns/scAce.

Modular Assembly of Pyrrolo[3,4-c]isoquinolines through Rh-Catalyzed Cascade C-H Activation/Annulation of O-Methyl Aryloximes with Maleimides.

An efficient and practical strategy for the construction of pyrrolo[3,4-c]isoquinolines via Rh(III)-catalyzed cascade C-H activation and subsequential annulation process from easily available O-methyl aryloximes and maleimides has been disclosed. This facile protocol does not require any inert atmosphere protection with good efficiency in a low loading of catalyst and exhibits good functional group tolerance and broad substrate scope. Notably, the as-prepared products show potential photophysical properties.

Base-Mediated Cascade Lactonization/1,3-Dipolar Cycloaddition Pathway for the One-Pot Assembly of Coumarin-Functionalized Pyrrolo[2,1-a]isoquinolines.

An elegant and highly concise strategy for the construction of coumarin-functionalized pyrrolo[2,1-a]isoquinolines from available propargylamines and isoquinolinium N-ylides has been disclosed. In this reaction, isoquinolinium N-ylides acted as a C2 synthon to form a coumarin ring as well as a 1,3-dipole to construct a pyrrole ring in a single pot. This cascade process involves 1,4-conjugate addition/lactonization/1,3-dipolar cycloaddition to construct four chemical bonds (one C-O bond and three C-C bonds) and two new heterocyclic skeletons. Additionally, most of these compounds showed good fluorescence properties and exhibited high molar extinction coefficient and large Stokes shifts.

A rhodium-catalyzed cascade C-H activation/annulation strategy for the expeditious assembly of pyrrolidinedione-fused 1,2-benzothiazines.

A cascade annulation strategy triggered by rhodium(III)-catalyzed C-H activation has been reported for the expeditious assembly of pyrrolidinedione-fused 1,2-benzothiazines from free NH-sulfoximines with maleimides under mild conditions. Without the need for inert atmosphere protection, a broad range of sulfoximines with maleimides were well tolerated, producing diverse fused-thiazine derivatives in moderate to good yields. Additionally, the late-stage transformation of the target product demonstrated the potential synthetic value of this protocol.

Predictors of the Rapid Progression in Prodromal Parkinson's Disease: A Longitudinal Follow-Up Study.

INTRODUCTION: Parkinson's disease (PD) is characterized by a prodromal phase preceding the onset of classic motor symptoms. The duration and clinical manifestations of prodromal PD vary widely, indicating underlying heterogeneity within this stage. This discrepancy prompts the question of whether specific factors contribute to the divergent rates of progression in prodromal PD. METHODS: This study included prodromal PD patients from the Parkinson's progression marker initiative. They were followed up to assess the disease progression. The data collected during the follow-up period were analyzed to identify potential predictors of rapid disease progression in prodromal PD. RESULTS: In this study, 61 individuals with prodromal PD were enrolled. Among them, 43 patients presented with both RBD and hyposmia, 17 had hyposmia alone, and 1 had RBD alone at baseline. 13 (21.3%) prodromal PD participants exhibited rapid disease progression, with two of these cases advancing to non-neurological diseases. Significant differences were observed between the rapid progression group and no rapid progression group in terms of MDS-UPDRS II score and UPSIT score. Longitudinal analysis showed a significant increase in the MDS-UPDRS III score and MDS-UPDRS total score in the rapid progression group. Regression analyses identified the MDS-UPDRS II score and UPSIT score as predictors of rapid disease progression in prodromal PD. CONCLUSION: Our study findings suggest that the MDS-UPDRS II score and UPSIT score may serve as clinical markers associated with rapid disease progression. Further research and development of precise biomarkers and advanced assessment methods are needed to enhance our understanding of prodromal PD and its progression patterns.

Identification of Key Molecular Pathways and Associated Genes as Targets to Overcome Radiotherapy Resistance Using a Combination of Radiotherapy and Immunotherapy in Glioma Patients.

Recent mechanistic studies have indicated that combinations of radiotherapy (RT) plus immunotherapy (via CSF-1R inhibition) can serve as a strategy to overcome RT resistance and improve the survival of glioma mice. Given the high mortality rate for glioma, including low-grade glioma (LGG) patients, it is of critical importance to investigate the mechanism of the combination of RT and immunotherapy and further translate the mechanism from mouse studies to improve survival of RT-treated human glioma patients. Using the RNA-seq data from a glioma mouse study, 874 differentially expressed genes (DEGs) between the group of RT-treated mice at glioma recurrence and the group of mice with combination treatment (RT plus CSF-1R inhibition) were translated to the human genome to identify significant molecular pathways using the KEGG enrichment analysis. The enrichment analysis yields statistically significant signaling pathways, including the phosphoinositide 3-kinase (PI3K)/AKT pathway, Hippo pathway, and Notch pathway. Within each pathway, a candidate gene set was selected by Cox regression models as genetic biomarkers for resistance to RT and response to the combination of RT plus immunotherapies. Each Cox model is trained using a cohort of 295 RT-treated LGG patients from The Cancer Genome Atlas (TCGA) database and validated using a cohort of 127 RT-treated LGG patients from the Chinese Glioma Genome Atlas (CGGA) database. A four-DEG signature (ITGB8, COL9A3, TGFB2, JAG1) was identified from the significant genes within the three pathways and yielded the area under time-dependent ROC curve AUC = 0.86 for 5-year survival in the validation set, which indicates that the selected DEGs have strong prognostic value and are potential intervention targets for combination therapies. These findings may facilitate future trial designs for developing combination therapies for glioma patients.

Construction of C-S and C-Se Bonds from Unstrained Ketone Precursors under Photoredox Catalysis.

A mild photoredox catalyzed construction of sulfides, disulfides, selenides, sulfoxides and sulfones from unstrained ketone precursors is introduced. Combination of this deacylative process with SN 2 or coupling reactions provides novel and convenient modular strategies toward unsymmetrical or symmetric disulfides. Reactivity studies favor a bromine radical that initiates a HAT (Hydrogen Atom Transfer) from the aminal intermediate resulting in expulsion of a C-centered radical that is intercepted to make C-S and C-Se bonds. Gram scale reactions, broad substrate scope and tolerance towards various functional groups render this method appealing for future applications in the synthesis of organosulfur and selenium complexes.

Cascade Annulation Strategy for Expeditious Assembly of Hydroxybenzo[c]chromen-6-ones and Their Photophysical Property Studies.

A 1,8-diazabicyclo[5.4.0]undec-7-ene-promoted cascade double-annulation of ortho-alkynyl quinone methide (in situ generated from modular propargylamine) for constructing of 2-aryl-4-hydroxybenzo[c]chromen-6-ones is developed. This synthetic strategy offers remarkable operational simplicity as it allows the use of benchtop-grade solvents without the need for predrying measures and inert atmosphere protection. Additionally, it demonstrates good functional group compatibility. The photophysical properties of these compounds were also examined, revealing bright fluorescence with high quantum yields.

Synthesis of arene-functionalized fused heterocyclic scaffolds via a regioselective cascade 1,4-conjugate addition/5-exo-dig annulation strategy.

Facile access to furan fused heterocyclic scaffolds through a regioselective cascade reaction of propargylamines with 4-hydroxy-2H-pyran-2-ones and 4-hydroxy-6-methylpyridin-2(1H)-one has been achieved. This cascade reaction presumably involves the formation of ortho-alkynyl quinone methide (o-AQM), 1,4-conjugate addition, followed by regioselective 5-exo-dig annulation, and a 1,3-H shift process. Moreover, the reaction provides a new and efficient method for the synthesis of highly sterically congested 3-phenolic furo[3,2-c]pyran-4-ones and furo[3,2-c]pyridin-4(5H)-ones by the formation of a furan ring from readily available starting materials in good to high yields (50-82%) with broad functional group compatibility in a single step. Significantly, the strategy described here is easily scalable and several useful synthetic transformations of the prepared arene-functionalized 4H-furo[3,2-c]pyran-4-ones were also performed.

Association between vertebrobasilar artery geometry and vertebrobasilar stenosis, recurrence, and death in posterior circulation stroke and transient ischemic attack.

BACKGROUND: Intracranial atherosclerosis is one of the primary causes of posterior circulation stroke and transient ischemic attack (TIA), particularly in people of South and East Asian heritage. Focal vessel geometry may play a role in atherosclerosis progression. Thus, we investigated the relevance of vertebrobasilar artery (VBA) geometry and vertebrobasilar atherosclerotic stenosis, recurrence, and death in posterior circulation stroke and TIA. METHODS: Four hundred and twenty patients with posterior circulation ischemic stroke or TIA were included. The VBA geometric features, comprising the geometric configurations (Tuning fork, Walking, Lambda, and No confluence), vascular bends (multi-bending and oligo-bending), and VBA stenosis degrees, were defined based on computed tomography angiography (CTA) images. Recurrence of stroke or TIA and death were assessed through a 1-year follow-up. Additionally, the relationship between VBA geometric features, VBA stenosis, and prognosis were analyzed. RESULTS: Walking type and vascular multi-bending showed significant associations with more severe VBA stenosis and distribution, and these were also more frequently observed in patients with large-artery atherosclerosis (LAA) stroke (all P < 0.05). Sixty-four patients exhibited recurrent stroke or TIA, and 31 died during the 1-year follow-up. In the binary logistic regression analysis, Walking type (P = 0.018), Lambda type (P = 0.021), and multi-bending type (P = 0.004) were found to be independently associated with stroke recurrence, while No confluence type was independently associated with death (P = 0.010). CONCLUSIONS: The geometric characteristics of the VBA are associated with vertebrobasilar stenosis, LAA stroke, 1-year recurrence, and death in posterior circulation stroke and TIA. VBA geometry may be used to stratify the risk of stroke and TIA in the posterior circulation.

Substituent-Controllable Cascade Regioselective Annulation of ß-Enaminones with N-Sulfonyl Triazoles for Modular Access to Imidazoles and Pyrroles.

A controllable synthesis of trisubstituted imidazoles and pyrroles has been developed through rhodium(II)-catalyzed regioselective annulation of N-sulfonyl-1,2,3-trizaoles with ß-enaminones. The imidazole ring was formed through a 1,1-insertion of the N-H bond to α-imino rhodium carbene, followed by a subsequent intramolecular 1,4-conjugate addition. This occurred when the α-carbon atom of the amino group was bearing a methyl group. Additionally, the pyrrole ring was constructed by utilizing a phenyl substituent and undergoing intramolecular nucleophilic addition. The mild conditions, good tolerance towards functional groups, gram-scale synthesis capability, and ability to undergo valuable transformations of the products qualify this unique protocol as an efficient tool for the synthesis of N-heterocycles.

Higher serum albumin-corrected calcium levels are associated with revascularization and poor outcome after mechanical thrombectomy.

BACKGROUND: Serum calcium abnormalities have been determined to be associated with the risk and outcome of stroke. The aim of the present study was to examine the associations of serum calcium with vascular recanalization, symptomatic intracranial haemorrhage and functional outcome in stroke patients after mechanical thrombectomy. METHODS: A total of 192 patients treated with mechanical thrombectomy for anterior circulation large vessel occlusion were consecutively included from August 2017 to June 2021. Serum calcium levels were measured on admission, and albumin-corrected calcium levels were calculated for subsequent analysis. Successful arterial revascularization was defined as a modified Thrombolysis in Cerebral Infarction scale score ≥ 2b. Symptomatic intracranial haemorrhage was assessed according to the European Cooperative Acute Stroke Study (ECASS) III criteria. Poor functional outcome was defined as a modified Rankin Scale score > 2 at 3 months. RESULTS: Patients with poor outcomes had higher albumin-corrected calcium levels than patients with good outcomes before (2.20 (2.10, 2.30) mmol/L vs. 2.13 (2.04, 2.24) mmol/L, P = 0.002), and after adjusting for other factors (AOR 95% CI, 1.812 (1.253, 2.621), P = 0.002). Patients with unsuccessful recanalization had higher albumin-corrected calcium levels than those with recanalization (2.26 (2.09, 2.46) mmol/L vs. 2.17 (2.07, 2.27) mmol/L, P = 0.029), and after adjusting for other factors (AOR 95% CI, 2.068 (1.214, 3.524)), P = 0.008). No association was found between albumin-corrected calcium and symptomatic intracranial haemorrhage. CONCLUSIONS: Higher serum albumin-corrected calcium levels are independently associated with revascularization and poor outcome in stroke patients after mechanical thrombectomy.

Rh-Catalyzed Cascade C-H Activation/Annulation of N-Hydroxybenzamides and Propargylic Acetates for Modular Access to Isoquinolones.

A sequential Rh(III)-catalyzed C-H activation/annulation of N-hydroxybenzamides with propargylic acetates leading to the formation of NH-free isoquinolones is described. This reaction proceeds through a sequential C-H activation/alkyne insertion/intramolecular annulation/N-O bond cleavage procedure, affording a broad spectrum of products with diverse substituents in moderate-to-excellent yields. Notably, this protocol features the simultaneous formation of two new C-C/C-N bonds and one heterocycle in one pot with the release of water as the sole byproduct.

Radical-Induced Cascade Annulation/Hydrocarbonylation for Construction of 2-Aryl-4H-chromen-4-ones.

A robust metal- and solvent-free cascade radical-induced C-N cleavage/intramolecular 6-endo-dig annulation/hydrocarbonylation for the synthesis of the valuable 2-aryl-4H-chromen-4-ones is described. This practical synthesis strategy utilizes propargylamines and air as the oxygen source and green carbonylation reagent, in which propargylamines are activated by the inexpensive and available dimethyl 2,2'-azobis(2-methylpropionate) (AIBME) and (PhSe)2 as the radical initiators. This simple and green protocol features wide substrate adaptability, good functional group tolerance, and amenability to scaling up and derivatizations.

Rh(III)-Catalyzed Cascade Nucleophilic Addition/Annulation of 2-Diazo-1,3-diketones with 1,3-Dicarbonyl Compounds To Access 6,7-Dihydrobenzofuran-4(5H)-ones.

A Rh(III)-catalyzed cascade nucleophilic addition/intramolecular annulation of 2-diazo-1,3-diketones with 1,3-dicarbonyl compounds (e.g., 1,3-diketones and ß-keto esters) is achieved to afford 6,7-dihydrobenzofuran-4(5H)-ones in up to 91% yields. Notably, a wide range of substrates and functional groups were well-tolerated under the optimized reaction conditions to give desired products in moderate to excellent yields with release of N2 and H2O as byproducts. Moreover, the method described is scalable and adaptable to late-stage functionalization.

Copper-Catalyzed Cascade 1,4-Addition/Annulation/Hydrolysis of Propargylamines with 2-Hydroxynaphthalene-1,4-diones: Direct Formation of 12-Phenacyl-11H-benzo[b]xanthenes.

A novel and versatile approach to construct 12-phenacyl-11H-benzo[b]xanthene-6,11(12H)-dione derivatives through copper-catalyzed cascade reaction of propargylamines with 2-hydroxynaphthalene-1,4-diones has been developed. The procedure is proposed to go through a sequence of 1,4-conjugate addition, intramolecular nucleophilic addition/dehydration, and hydrolysis of alkyne followed by an enol-ketone tautomerization. The reaction provides a new and highly efficient method for the synthesis of 12-phenacyl-11H-benzo[b]xanthene-6,11(12H)-diones by formation of three new bonds and one heterocycle from readily available starting materials in good to high yields (70-88%) with broad functional group compatibility in a single step.

Construction of isoxazolone-fused phenanthridines via Rh-catalyzed cascade C-H activation/cyclization of 3-arylisoxazolones with cyclic 2-diazo-1,3-diketones.

A Rh(iii)-catalyzed cascade C-H activation/intramolecular cyclization of 3-aryl-5-isoxazolones with cyclic 2-diazo-1,3-diketones was described, leading to the formation of isoxazolo[2,3-f]phenanthridine skeletons. The protocol features the simultaneous one-pot formation of two new C-C/C-N bonds and one heterocycle in moderate-to-good yields with good functional group compatibility. It is amenable to large-scale synthesis and further transformation.

Rh-Catalyzed C-H activation/intramolecular condensation for the construction of benzo[f]pyrazolo[1,5-a][1,3]diazepines.

A novel and mild Rh(iii)-catalyzed C-H activation/intramolecular condensation of 1-aryl-1H-pyrazol-5-amines with cyclic 2-diazo-1,3-diketones was developed, giving access to various important benzo[f]pyrazolo[1,5-a][1,3]diazepine scaffolds through sequential C-C/C-N bond formation in a one-pot procedure under additive- and oxidant-free conditions. Furthermore, 3-([1,1'-biphenyl]-2-ylamino)-2-ethoxycyclohex-2-enones can be obtained in good yields by constructing C-O and C-N bonds through 1,1'-insertion, dehydration, and isomerization processes.

Synthesis of unsymmetrical urea derivatives via one-pot sequential three-component reactions of cyclic 2-diazo-1,3-diketones, carbodiimides, and 1,2-dihaloethanes.

A novel and efficient multicomponent reaction of cyclic 2-diazo-1,3-diketones, carbodiimides, and 1,2-dihaloethanes has been developed, and it leads to unsymmetrical urea derivatives with good yields in a single operation. This transformation involves the cascade formation of C-X (X = Cl, Br, I), C-N and C[double bond, length as m-dash]O bonds through halogenation, nucleophilic addition, ring-opening, and enol-ketone tautomerization processes. This protocol is step- and atom-economical; 1,2-dihaloethane was used as an easily available halogenated reagent, and it is amenable to different functional groups.