Consensus-based clustering of single cells by reconstructing cell-to-cell dissimilarity.

The development of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) technology has led to great opportunities for the identification of heterogeneous cell types in complex tissues. Clustering algorithms are of great importance to effectively identify different cell types. In addition, the definition of the distance between each two cells is a critical step for most clustering algorithms. In this study, we found that different distance measures have considerably different effects on clustering algorithms. Moreover, there is no specific distance measure that is applicable to all datasets. In this study, we introduce a new single-cell clustering method called SD-h, which generates an applicable distance measure for different kinds of datasets by optimally synthesizing commonly used distance measures. Then, hierarchical clustering is performed based on the new distance measure for more accurate cell-type clustering. SD-h was tested on nine frequently used scRNA-seq datasets and it showed great superiority over almost all the compared leading single-cell clustering algorithms.

MicrobeTCM: A comprehensive platform for the interactions of microbiota and traditional Chinese medicine.

Thanks to the advancements in bioinformatics, drugs, and other interventions that modulate microbes to treat diseases have been emerging continuously. In recent years, an increasing number of databases related to traditional Chinese medicine (TCM) or gut microbes have been established. However, a database combining the two has not yet been developed. To accelerate TCM research and address the traditional medicine and micro ecological system connection between short board, we have developed the most comprehensive micro-ecological database of TCM. This initiative includes the standardization of the following advantages: (1) A repeatable process achieved through the standardization of a retrieval strategy to identify literature. This involved identifying 419 experiment articles from PubMed and six authoritative databases; (2) High-quality data integration achieved through double-entry extraction of literature, mitigating uncertainties associated with natural language extraction; (3) Implementation of a similar strategy aiding in the prediction of mechanisms of action. Leveraging drug similarity, target entity similarity, and known drug-target entity association, our platform enables the prediction of the effects of a new herb or acupoint formulas using the existing data. In total, MicrobeTCM includes 171 diseases, 725 microbes, 1468 herb-formulas, 1032 herbs, 15780 chemical compositions, 35 acupoint-formulas, and 77 acupoints. For further exploration, please visit https://www.microbetcm.com.

A previously healthy 3-year-old female with hypertension, proteinuria, and hypercalciuria.

A 3-year-old female patient with no significant medical history presented to her pediatrician with foamy urine. Initial testing revealed moderate proteinuria on qualitative testing, although she was incidentally noted to have severe hypertension (240/200 mmHg). Physical examination of the carotid and femoral areas revealed significant systolic vascular murmurs. Labs showed elevated serum creatinine, hypokalemia, metabolic alkalosis, elevated renin and aldosterone and hypercalciuria. Echocardiography identified ventricular hypertrophy. Computed tomography (CT) of the abdomen and magnetic resonance angiography of the head showed multiple tortuous or interrupted arteries and multiple calcifications in the renal sinus area. B-mode ultrasonography suggested thickening of the carotid and femoral artery walls, with numerous spotted calcifications. Genetic testing revealed that ABCC6 had a complex heterozygous mutation (exon 24: c.3340C > T and intron 30: c.4404-1G > A). Our panel of experts reviewed the evaluation of this patient with hypertension, proteinuria, hypercalciuria, and vascular abnormalities as well as the diagnosis and appropriate management of a rare disease.

Abnormal microstructure of corpus callosum in children with primary nocturnal enuresis: a DTI study.

Primary nocturnal enuresis (PNE) is a common childhood disorder with abnormal sleep or arousal. The corpus callosum (CC) continues to develop into adulthood and plays an important role in sleep arousal. This study aimed to evaluate the microstructure of the CC in children with PNE. Diffusion tensor imaging (DTI) indices were extracted throughout the CC and its seven subregions were compared between the children with PNE and healthy children (HC). The correlation between abnormal DTI indices of the CC and cognitive condition was also tested. Compared to HC, decreased fiber number (NF) (F = 8.492, PFDR = 0.032) and fractional anisotropy (FA) value (F = 8.442, PFDR = 0.040) were found in the posterior midbody of the CC, increased RD was found in the posterior midbody (F = 6.888, PFDR = 0.040) and isthmus (F = 7.967, PFDR = 0.040) in children with PNE. The reduction of FA value was more obvious in boys than girls with PNE. In children with PNE, there was a significant positive correlation between the NF of the posterior midbody and full IQ (r = 0.322, P = 0.025) and between the FA value and the general knowledge memory (r = 0.293, P = 0.043). This study provides imaging evidence for abnormalities in the microstructure of the CC in children with PNE, especially in male PNE, which might affect the children's cognitive performance.

Application of CuFeLDH-NCNT in ultrasound-assisted-Fenton-like process for removing ciprofloxacin from aqueous solutions.

In this study, the mesoporous material NCNT was prepared by treating carbon nanotubes (CNT) with hydrazine and subsequently loaded with Cu-Fe layered double hydroxide (CuFeLDH) to create a multiphase catalyst (CuFeLDH-NCNT). Its application as a multiphase catalyst was investigated in an ultrasound-assisted Fenton process for ciprofloxacin (CIP) degradation in aqueous solution. In addition, the impacts of catalyst dosage, ultrasonic power, H2O2 dosage, and beginning pH on CIP removal efficiency were carefully evaluated to maximize the removal efficiency of CIP. The findings indicated that the elimination rate of the initial CIP concentration of 20 mg/L surpassed 94.66% after a mere 100 min, while the TOC degradation rate was 70.4%. The high removal rate was due to the synergistic action between the nanoparticles, H2O2, and ultrasonography. The degradation intermediates of CIP were examined, and putative degradation pathways and mechanisms were postulated.

Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data.

BACKGROUND: Advances in single-cell RNA-seq technology have led to great opportunities for the quantitative characterization of cell types, and many clustering algorithms have been developed based on single-cell gene expression. However, we found that different data preprocessing methods show quite different effects on clustering algorithms. Moreover, there is no specific preprocessing method that is applicable to all clustering algorithms, and even for the same clustering algorithm, the best preprocessing method depends on the input data. RESULTS: We designed a graph-based algorithm, SC3-e, specifically for discriminating the best data preprocessing method for SC3, which is currently the most widely used clustering algorithm for single cell clustering. When tested on eight frequently used single-cell RNA-seq data sets, SC3-e always accurately selects the best data preprocessing method for SC3 and therefore greatly enhances the clustering performance of SC3. CONCLUSION: The SC3-e algorithm is practically powerful for discriminating the best data preprocessing method, and therefore largely enhances the performance of cell-type clustering of SC3. It is expected to play a crucial role in the related studies of single-cell clustering, such as the studies of human complex diseases and discoveries of new cell types.

Combined Relativistic Ab Initio Multireference and Experimental Study of the Electronic Structure of Terbium Luminescent Compound.

A new terbium (III) luminescent compound {[Tb2(PDC)2(ox)(H2O)4](H2O)2}n was synthesized by the self-assembly of Tb3+ ions with 3,5-pyridinedicarboxylate (PDC) and oxalate (ox) ligands and characterized by fluorescence spectroscopy and single-crystal X-ray diffraction. The density functional theory (DFT) and high-level correlated ab initio wave function methods with Spin-Orbit Coupling correction (CASSCF/SO and CAS-NEVPT2/SOC) were successfully applied to predict the absorption and emission spectra of this strongly correlated lanthanide system in excellent agreement with the experimental results.

Cervical dilation balloon combined with intravenous drip of oxytocin for induction of term labor: a multicenter clinical trial.

OBJECTIVE: This study aimed to investigate the effectiveness and safety of a method combining double-balloon catheter for cervical ripening and intravenous drip of oxytocin on the induction of term labor, providing the reference for clinical safety. METHODS: A total of 120 pregnant women with a gestation between 37+0 and  41+6 weeks, indications of labor induction, singleton pregnancy with cephalic presentation were enrolled. The patients were divided into the research group receiving cervical dilation balloon combined with intravenous drip of oxytocin and the control group receiving an intravenous drip of oxytocin at a concentration of 0.5% for labor induction (n = 60 for each). The effectiveness and safety of labor induction were evaluated by the rates of successful cervical ripening promotion and labor induction, as well as the vaginal delivery rate, induced labor time, total duration of labor, the total amount of postpartum hemorrhage within 24 h after giving birth, the incidences of postpartum hemorrhage, cervical laceration, puerperal infection and neonatal outcomes. RESULTS: There was no statistical difference in the basal demographic and clinical characteristics, including ages, gestational weeks, delivery times and Bishop scores at admission between two groups. The rate of successful cervical ripening promotion (research vs. control = 90.00% vs. 55.00%), the rate of successful induction (95.00% vs. 40.00%), the vaginal delivery rate (93.33% vs. 63.33%), the induced labor time (15.03 ± 5.40 vs. 30.68 ± 10.82 h), and the total duration of labor (8.12 ± 2.65 vs. 15.01 ± 6.06 h) were significantly different between two groups (all P < 0.05). There was no significant difference in the total amount of postpartum hemorrhage, incidences of postpartum hemorrhage, cervical laceration, puerperal infection as well as the neonatal outcomes, including neonatal weight, neonatal asphyxia and incidence of meconium aspiration syndrome between two groups. CONCLUSIONS: Compared to labor induction of oxytocin, the method combining double-balloon catheter for cervical ripening and intravenous drip of oxytocin for the induction of term labor has a higher vaginal delivery rate, shorter total duration of labor, and does not increase the incidences of postpartum hemorrhage and neonatal infection, which is a more effective and safer method for induction of term labor.

Tf2NH-Catalyzed Formal [3 + 2] Cycloaddition of Ynamides with Dioxazoles: A Metal-Free Approach to Polysubstituted 4-Aminooxazoles.

An unprecedented Tf2NH-catalyzed formal [3 + 2] cycloaddition of ynamides with dioxazoles was developed to construct various polysubstituted 4-aminooxazoles. This approach features a metal-free catalytic bimolecular assembly of oxazole motifs, a low-cost catalyst, exceptionally mild reaction conditions, a very short reaction time, a broad substrate scope, and high efficiency. This metal-free protocol may find applications in pharmaceutical-oriented synthesis.

Ruthenium-Catalyzed [3 + 2] Cycloaddition of 2H-Azirines with Alkynes: Access to Polysubstituted Pyrroles.

A ruthenium-catalyzed intermolecular [3 + 2] cycloaddition of 2H-azirines and activated alkynes is reported, which provides polysubstituted pyrroles in moderate to good yields. This approach features a C-N bond cleavage of 2H-azirines by a ruthenium catalyst. The results of this study would provide a complementary method to synthesize polysubstituted pyrroles from the known 2H-azirine approaches and advance 2H-azirine chemistry.

Ruthenium-Catalyzed C-C Bond Cleavage of 2H-Azirines: A Formal [3+2+2] Cycloaddition to Fused Azepine Skeletons.

2H-azirines can serve as three-atom synthons by C-C bond cleavage, however, it involves a high energy barrier under thermal conditions (>50.0 kcal mol(-1) ). Reported is a ruthenium-catalyzed [3+2+2] cycloaddition reaction of 2H-azirines with diynes, thus leading to the formation of fused azepine skeletons. This approach features an unprecedented metal-catalyzed C-C bond cleavage of 2H-azirines at room temperature, and the challenging construction of aza-seven-membered rings from diynes. The results of this study provide a new reaction pattern for constructing nitrogen-containing seven-membered rings and may find applications in the synthesis of other complex heterocycles.

Seven New Tetrahydroanthraquinones from the Root of Prismatomeris connata and Their Cytotoxicity against Lung Tumor Cell Growth.

The root of Prismatomeris connata has been used in China for centuries as the medicinal herb "Huang Gen" (HG), but its phytochemicals or active ingredients are not well understood. In this study, we performed chemical analysis of the ethyl acetate fraction of a HG ethanol extract. We thus isolated seven new tetrahydroanthraquinones, prisconnatanones C-I (compounds 1-7) from the root of P. connata and identified their structures using spectroscopic analyses. Their absolute configurations were established by both modified Mosher's and Mo2OAc4 methods, and ORD techniques. Their cytotoxicity was tested in a panel of human lung tumor cells (H1229, HTB179, A549 and H520 cell lines). Prisconnatanone I (7) showed the highest activity, with an IC50 value ranging from 2.7 µM to 3.9 µM in the suppression of tumor cell growth, and the others with chelated phenolic hydroxyls exhibited relatively lower activity (IC50: 8-20 µM). In conclusion, these data suggest that some of the natural tetrahydroanthraquinones in HG are bioactive, and hydroxylation at C-1 significantly increases the cytotoxicity of these compounds against lung tumor cell growth.

Rhodium-Catalyzed C-H Annulation of Nitrones with Alkynes: A Regiospecific Route to Unsymmetrical 2,3-Diaryl-Substituted Indoles.

The direct C-H annulation of anilines or related compounds with internal alkynes provides straightforward access to 2,3-disubstituted indole products. However, this transformation proceeds with poor regioselectivity in the synthesis of unsymmetrically 2,3-diaryl substituted indoles. Herein, we report the rhodium(III)-catalyzed C-H annulation of nitrones with symmetrical diaryl alkynes as an alternative method to prepare 2,3-diaryl-substituted N-unprotected indoles with two different aryl groups. One of the aryl substituents is derived from N=C-aryl ring of the nitrone and the other from the alkyne substrate, thus providing the indole products with exclusive regioselectivity.

From propargylamides to oxazole derivatives: NIS-mediated cyclization and further oxidation by dioxygen.

NIS-mediated iodocyclization of N-sulfonyl propargylamides for the synthesis of various oxazolidines and iodoalkylidenedihydrooxazoles via a 5-exo-dig process is developed. The resulting iodoalkylidenedihydrooxazoles can be further transformed into the corresponding oxazoles in the presence of dioxygen.

DABCO-catalyzed synthesis of trifluoromethylated furans from propargyl alcohols and methyl 2-perfluoroalkynoate.

The DABCO-catalyzed reaction of propargyl alcohols with methyl 2-perfluoroalkynoate to give trifluoromethylated furans in up to 98% yield under mild conditions has been developed. The established allene-enol and control experiments indicate that the reaction should proceed through a Michael addition and Claisen rearrangement/cyclization process.

Classifications of clinical and bowel morphological changes and their relationship with characteristics of patients with incarcerated groin hernias.

BACKGROUND: There is currently no grading standard for the degree of clinical and bowel morphological changes. The objective of this study was to define clinical and bowel morphological classifications and investigate the possible relationship with the characteristics of patients with incarcerated groin hernias. MATERIAL AND METHODS: We retrospectively studied 195 patients who underwent emergency hernia repair with simultaneous bowel resection between January 1992 and January 2012. We classified the degree of clinical and bowel morphological changes into 3 grades based on the incarceration time, intestinal morphology after damage, hernia sac integrity, degree of inflammation, and the presence/absence of bacterial growth, peritonitis signs, mechanical obstruction, cellulitis, and systemic shock. We also recorded patient characteristics and analyzed their relationships with these degrees according to our grading system. RESULTS: We identified 134, 42, and 19 cases of Grades I, II, and III of clinical and bowel morphological changes, respectively. Pearson's chi-squared tests revealed that advanced age (P=0.001), presence of comorbid disease (P=0.002), and high American Society of Anesthesiologists (ASA) score (P=0.017) were related to the degree. Morbidity and mortality also showed significant relationships with the degree (P<0.001, P=0.005, respectively), especially with regard to post-operative infection. CONCLUSIONS: The proposed 3-stage classifications of clinical and bowel morphological changes can be used to objectively reflect the degree of bowel damage. Greater levels of the changes were associated with higher incidences of complications and increased mortality, especially for older patients with comorbid diseases and poor ASA scores. Urgent surgery should be performed to avoid bowel damage exacerbation.

Community structure and succession regulation of fungal consortia in the lignocellulose-degrading process on natural biomass.

The study aims to investigate fungal community structures and dynamic changes in forest soil lignocellulose-degrading process. rRNA gene clone libraries for the samples collected in different stages of lignocellulose degradation process were constructed and analyzed. A total of 26 representative RFLP types were obtained from original soil clone library, including Mucoromycotina (29.5%), unclassified Zygomycetes (33.5%), Ascomycota (32.4%), and Basidiomycota (4.6%). When soil accumulated with natural lignocellulose, 16 RFLP types were identified from 8-day clone library, including Basidiomycota (62.5%), Ascomycota (36.1%), and Fungi incertae sedis (1.4%). After enrichment for 15 days, identified 11 RFLP types were placed in 3 fungal groups: Basidiomycota (86.9%), Ascomycota (11.5%), and Fungi incertae sedis (1.6%). The results showed richer, more diversity and abundance fungal groups in original forest soil. With the degradation of lignocellulose, fungal groups Mucoromycotina and Ascomycota decreased gradually, and wood-rotting fungi Basidiomycota increased and replaced the opportunist fungi to become predominant group. Most of the fungal clones identified in sample were related to the reported lignocellulose-decomposing strains. Understanding of the microbial community structure and dynamic change during natural lignocellulose-degrading process will provide us with an idea and a basis to construct available commercial lignocellulosic enzymes or microbial complex.

Crystal structure of catena-poly[[di-aqua(4,5-di-aza-fluoren-9-one-κ(2) N,N')cadmium]-µ-2-hydroxy-5-sulfonato-benzoato-κ(3) O (1),O (1'):O (5)].

In the polymeric title compound, [Cd(C7H4O6S)(C11H6N2O)(H2O)2] n , the Cd(2+) atom is seven-coordinated by two water O atoms, by three O atoms from two 2-hy-droxy-5-sulfonato-benzoate (Hssal(2-)) ligands and by two N atoms from a 4,5-di-aza-fluoren-9-one (Dafo) ligand in a distorted penta-gonal-bipyramidal geometry. The Cd(2+) atoms are monodentately coordinated by the sulfonate group of one Hssal(2-) ligand and bidentately coordinated by the carboxyl-ate group of another Hssal(2-) ligand, generating zigzag chains running parallel to [010]. The chains are linked by O-H⋯O hydrogen bonds into a three-dimensional architecture.

Crystal structure of poly[µ6-adipato-di-aquadi-µ2-oxalato-didysprosium(III)].

In the title coordination polymer, [Dy2(C6H8O4)(C2O4)2(H2O)2] n , the asymmetric unit consists of one Dy(3+) cation, one half of an adipate anion, two halves of oxalate anions and one coordinating water mol-ecule. The adipate and oxalate ions are located on centres of inversion. The Dy(3+) cation has a distorted tricapped trigonal-prismatic geometry and is coordinated by nine O atoms, four belonging to three adipate anions, four to two oxalate anions and one from an aqua ligand. The cations are bridged by adipate ligands, generating a two-dimensional network parallel to (010). This network is further extended into three dimensions by coordination of the rigid oxalate ligands and is further consolidated by O-H⋯O hydrogen bonds. A part of the adipate anion is disordered over two positions in a 0.75:0.25 ratio.

Rhodium-catalyzed cyclization of diynes with nitrones: a formal [2+2+5] approach to bridged eight-membered heterocycles.

N-aryl-substituted nitrones were employed as five-atom coupling partners in the rhodium-catalyzed cyclization with diynes. In this reaction, the nitrone moiety served as a directing group for the catalytic C-H activation of the N-aryl ring. This formal [2+2+5] approach allows rapid access to bridged eight-membered heterocycles with broad substrate scope. The results of this study may provide new insight into the chemistry of nitrones and find applications in the synthesis of other heterocycles.