HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer.

Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease. Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.

Regiodivergent Remote C-H Functionalization by Tuning Template Geometry.

For transition-metal-catalyzed C-H functionalization, precise differentiation between remote adjacent C(sp2)-H bonds remains a long-standing challenge. Here, the template structure-directivity relationship on remote C-H functionalization of arenes was experimentally and computationally studied. By using geometry-tunable templates, Pd-catalyzed remote meta- and para-C-H activation of benzoic acids was achieved with high site selectivity.

Palladium-catalyzed regio- and stereo-selective phosphination of cyclic biarylsulfonium salts to access atropoisomeric phosphines.

A palladium-catalyzed regio- and stereo-selective phosphination of cyclic biarylsulfonium salts (racemic) with HPAr3Ar4 for straightforward synthesis of atropoisomeric phosphines (P,S-ligands) bearing a stereogenic axis or both a stereogenic axis and a P-stereogenic center is reported. The high reactivity and regio- and stereo-selectivity originate from the torsional strain release and palladium catalysis, and the construction of a P-stereogenic center is enabled by an efficient dynamic kinetic resolution. The high performance of the nascent P,S-ligands has been demonstrated in palladium-catalyzed asymmetric allylic substitutions, indicating the great potential of the present methodology.

Highly Diastereo- and Enantioselective Synthesis of Chiral Cyclohexylphosphines by Cu-Catalyzed Phosphination-Aldol Cyclization of Ketone-Enamides.

A highly diastereo- and enantioselective phosphinative cyclization of ketone-enamides with secondary diarylphosphines enabled by copper catalysis is reported, providing a range of chiral tertiary cyclohexylphosphines bearing three contiguous stereogenic centers in high yields. This asymmetric phosphination-aldol cyclization protocol can also be extended to desymmetrization of dione-enamides to create four contiguous stereogenic centers in a highly selective manner.

Dithiolation of Alkenyl Sulfonium Salts with Arylthiols to Access 1,2-Dithioalkanes.

A dithiolation of alkenyl sulfonium salts with arylthiols is described, affording a series of 1,2-dithioalkanes in high yields. This protocol features mild and catalyst-free conditions and involves the formation of two C-S bonds sequentially via the regioselective addition of an arylthiol to the unsaturated C═C bonds, followed by the attack of another arylthiol to form 1,2-dithioalkanes exclusively.

Stereoselective Synthesis of Tri- and Tetrasubstituted Allylsilanes via Copper-Catalyzed Decarboxylative Silylation of Vinylethylene Carbonates.

Herein, a stereoselective copper-catalyzed decarboxylative silylation of readily available vinylethylene carbonates (VECs) with PhMe2Si-Bpin is reported, affording a wide range of tri- and tetrasubstituted allylsilanes in moderate to high yields with E-selectivity. This protocol was characterized by high stereoselectivity, broad substrate scope, operational simplicity, and mild reaction conditions, which were amenable to diverse derivatizations and gram-scale synthesis.

Highly Regioselective Dichalcogenation of Alkenyl Sulfonium Salts to Access 1,1-Dichalcogenalkenes.

An unprecedented geminal olefinic dichalcogenation of alkenyl sulfonium salts with dichalcogenides ArYYAr (Y = S, Se, Te) is reported, providing various trisubstituted 1,1-dichalcogenalkenes [Ar1CH = C(YAr2)2] in a highly selective manner under mild and catalyst-free conditions. The key process involves the formation of two geminal olefinic C-Y bonds via sequential C-Y cross-coupling and C-H chalcogenation. A mechanistic rationale is further supported by control experiments and density functional theory calculations.

Predicting visual acuity with machine learning in treated ocular trauma patients.

AIM: To predict best-corrected visual acuity (BCVA) by machine learning in patients with ocular trauma who were treated for at least 6mo. METHODS: The internal dataset consisted of 850 patients with 1589 eyes and an average age of 44.29y. The initial visual acuity was 0.99 logMAR. The test dataset consisted of 60 patients with 100 eyes collected while the model was optimized. Four different machine-learning algorithms (Extreme Gradient Boosting, support vector regression, Bayesian ridge, and random forest regressor) were used to predict BCVA, and four algorithms (Extreme Gradient Boosting, support vector machine, logistic regression, and random forest classifier) were used to classify BCVA in patients with ocular trauma after treatment for 6mo or longer. Clinical features were obtained from outpatient records, and ocular parameters were extracted from optical coherence tomography images and fundus photographs. These features were put into different machine-learning models, and the obtained predicted values were compared with the actual BCVA values. The best-performing model and the best variable selected were further evaluated in the test dataset. RESULTS: There was a significant correlation between the predicted and actual values [all Pearson correlation coefficient (PCC)>0.6]. Considering only the data from the traumatic group (group A) into account, the lowest mean absolute error (MAE) and root mean square error (RMSE) were 0.30 and 0.40 logMAR, respectively. In the traumatic and healthy groups (group B), the lowest MAE and RMSE were 0.20 and 0.33 logMAR, respectively. The sensitivity was always higher than the specificity in group A, in contrast to the results in group B. The classification accuracy and precision were above 0.80 in both groups. The MAE, RMSE, and PCC of the test dataset were 0.20, 0.29, and 0.96, respectively. The sensitivity, precision, specificity, and accuracy of the test dataset were 0.83, 0.92, 0.95, and 0.90, respectively. CONCLUSION: Predicting BCVA using machine-learning models in patients with treated ocular trauma is accurate and helpful in the identification of visual dysfunction.

CCT-Unet: A U-Shaped Network Based on Convolution Coupled Transformer for Segmentation of Peripheral and Transition Zones in Prostate MRI.

The accurate segmentation of prostate region in magnetic resonance imaging (MRI) can provide reliable basis for artificially intelligent diagnosis of prostate cancer. Transformer-based models have been increasingly used in image analysis due to their ability to acquire long-term global contextual features. Although Transformer can provide feature representations of the overall appearance and contour representations at long distance, it does not perform well on small-scale datasets of prostate MRI due to its insensitivity to local variation such as the heterogeneity of the grayscale intensities in the peripheral zone and transition zone across patients; meanwhile, the convolutional neural network (CNN) could retain these local features well. Therefore, a robust prostate segmentation model that can aggregate the characteristics of CNN and Transformer is desired. In this work, a U-shaped network based on the convolution coupled Transformer is proposed for segmentation of peripheral and transition zones in prostate MRI, named the convolution coupled Transformer U-Net (CCT-Unet). The convolutional embedding block is first designed for encoding high-resolution input to retain the edge detail of the image. Then the convolution coupled Transformer block is proposed to enhance the ability of local feature extraction and capture long-term correlation that encompass anatomical information. The feature conversion module is also proposed to alleviate the semantic gap in the process of jumping connection. Extensive experiments have been conducted to compare our CCT-Unet with several state-of-the-art methods on both the ProstateX open dataset and the self-bulit Huashan dataset, and the results have consistently shown the accuracy and robustness of our CCT-Unet in MRI prostate segmentation.

Suicide before and during the COVID-19 Pandemic: A Systematic Review with Meta-Analysis.

Synthesizing evidence to examine changes in suicide-related outcomes before and during the pandemic can inform suicide management during the COVID-19 crisis. We searched 13 databases as of December 2022 for studies reporting both the pre- and peri-pandemic prevalence of suicidal ideation, suicide attempts, or rate of death by suicide. A random-effects model was used to pool the ratio of peri- and pre-pandemic prevalence of suicidal ideation and attempt (Prevalence Ratio-PR) and rate of death by suicide (Rate Ratio; RR). We identified 51, 55, and 25 samples for suicidal ideation, attempt, and death by suicide. The prevalence of suicidal ideation increased significantly among non-clinical (PR = 1.142; 95% CI: 1.018-1.282; p = 0.024; k = 28) and clinical (PR = 1.134; 95% CI: 1.048-1.227; p = 0.002; k = 23) samples, and pooled estimates differed by population and study design. Suicide attempts were more prevalent during the pandemic among non-clinical (PR = 1.14; 95% CI: 1.053-1.233; p = 0.001; k = 30) and clinical (PR = 1.32; 95% CI: 1.17-1.489; p = 0.000; k = 25) participants. The pooled RR for death by suicide was 0.923 (95% CI: 0.84-1.01; p = 0.092; k = 25), indicating a nonsignificant downward trend. An upward trend of suicidal ideation and suicide attempts was observed during the COVID-19 pandemic, despite suicide rate remaining stable. Our findings suggest that timely prevention and intervention programs are highly needed for non-clinical adult population and clinical patients. Monitoring the real-time and long-run suicide risk as the pandemic evolves is warranted.

Prevalence of depressive and anxiety symptoms among Chinese older adults during the COVID-19 pandemic: A systematic review and meta-analysis.

Background: Estimating the prevalence of depressive and anxiety symptoms among older adults with different health conditions can inform mental health services for this population during the corona virus disease-2019 (COVID-19) pandemic. Method: A search of 12 scientific databases identified 17 studies with 11,237 Chinese older adults who were infected by COVID-19, were generally healthy, or had chronic illnesses. Meta-analysis was used to estimate the overall prevalence of depressive and anxiety symptoms in these three groups. Assessment criteria, region, and time phase of the pandemic were tested as sources of heterogeneity. Results: With an average risk of bias score of 6.71 (range = 6-8), the majority of included studies employed appropriate statistical methods, used validated measurement tools, and had adequate response rates; however, they might have deficiencies in sample frame, sampling method, and sample size. Within the COVID-19, general, and chronic illness groups, the prevalence of depressive symptoms was 27%, 26%, and 61%, respectively, and the prevalence of anxiety symptoms was 14%, 23%, and 85%, respectively. Among generally healthy older adults, anxiety was more prevalent during the Phase 2 (March-April 2020) of the pandemic compared with other time phases. Conclusions: The results have implications for addressing the mental health problems of Chinese older adults, especially those with chronic illnesses, during the COVID-19 pandemic.

Four-quadrant fast compressive tracking of breast ultrasound videos for computer-aided response evaluation of neoadjuvant chemotherapy in mice.

BACKGROUND AND OBJECTIVE: Neoadjuvant chemotherapy (NAC) is a valuable treatment approach for locally advanced breast cancer. Contrast-enhanced ultrasound (CEUS) potentially enables the assessment of therapeutic response to NAC. In order to evaluate the response accurately, quantitatively and objectively, a method that can effectively compensate motions of breast cancer in CEUS videos is urgently needed. METHODS: We proposed the four-quadrant fast compressive tracking (FQFCT) approach to automatically perform CEUS video tracking and compensation for mice undergoing NAC. The FQFCT divided a tracking window into four smaller windows at four quadrants of a breast lesion and formulated the tracking at each quadrant as a binary classification task. After the FQFCT of breast cancer videos, the quantitative features of CEUS including the mean transit time (MTT) were computed. All mice showed a pathological response to NAC. The features between pre- (day 1) and post-treatment (day 3 and day 5) in these responders were statistically compared. RESULTS: When we tracked the CEUS videos of mice with the FQFCT, the average tracking error of FQFCT was 0.65 mm, reduced by 46.72% compared with the classic fast compressive tracking method (1.22 mm). After compensation with the FQFCT, the MTT on day 5 of the NAC was significantly different from the MTT before NAC (day 1) (p = 0.013). CONCLUSIONS: The FQFCT improves the accuracy of CEUS video tracking and contributes to the computer-aided response evaluation of NAC for breast cancer in mice.

US FDA-approved therapeutic antibodies with high-concentration formulation: summaries and perspectives.

Thirty four (34) of the total US FDA approved 103 therapeutic antibody drugs, accounts for one third of the total approved mAbs, are formulated with high protein concentration (100 mg/mL or above) which are the focus of this article. The highest protein concentration of these approved mAbs is 200 mg/mL. The dominant administration route is subcutaneous (76%). Our analysis indicates that it may be rational to implement a platform formulation containing polysorbate, histidine and sucrose to accelerate high concentration formulation development for antibody drugs. Since 2015, the FDA approval numbers are significantly increased which account for 76% of the total approval numbers, i.e., 26 out of 34 highly concentrated antibodies. Thus, we believe that the high concentration formulations of antibody drugs will be the future trend of therapeutic antibody formulation development, regardless of the challenges of highly concentrated protein formulations.

A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.

Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3' noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.

[Corrigendum] Connexin 43 reduces susceptibility to sympathetic atrial fibrillation.

Following the publication of the above article, the authors have realized that the data shown in Fig. 3B were published previously in Fig 1A of following publication, on which several of were co­authors [Shu C, Huang W, Zeng Z, He Y, Luo B, Liu H, Li J and Xu J: Connexin 43 is involved in the sympathetic atrial fibrillation in canine and canine atrial myocytes. Anatol J Cardiol 18: 3­9, 2017]. This error arose inadvertently; the corrected version of Fig. 3, also containing the correct data for Fig. 3B, is shown opposite. The authors are grateful to the Editor of International Journal of Molecular Medicine for allowing them the opportunity to publish this Corrigendum, and stress that this error did not significantly influence either the results or the conclusions of the paper. Furthermore, the authors apologize to the readership for any inconvenience caused. [the original article was published in International Journal of Molecular Medicine 42: 1125-1133, 2018; DOI: 10.3892/ijmm.2018.3648].

The effects of acceptance and commitment therapy on the psychological and physical outcomes among cancer patients: A meta-analysis with trial sequential analysis.

OBJECTIVE: The current study used meta-analysis and trial sequential analysis to estimate the effects of Acceptance and Commitment Therapy (ACT) on the psychological and physical distress of cancer patients, and to identify potential moderators in this body of research. METHODS: A search of multiple databases in February 2020 identified 25 independent trials (17 randomized controlled trials, 8 non-randomized controlled trials; 2256 participants) on the effects of ACT among cancer patients. Trial sequential analysis (TSA) was used to determine whether the available evidence is sufficient to draw strong conclusions. RESULTS: ACT significantly reduced cancer patients' psychological distress (g = 0.88), and improved psychological flexibility (g = 0.58), quality of life (g = 1.19), and sense of hope (g = 2.17). TSA showed that there was sufficient evidence to obtain stable estimates of the effect of ACT on psychological distress and quality of life. Effect sizes for psychological distress were larger in studies conducted in eastern countries, in younger samples, and when therapy was of longer duration. CONCLUSION: Acceptance and Commitment Therapy can effectively improve the mental health of cancer patients, and can be applied to clinical practice as an effective psychological intervention. Researchers are encouraged to take into account stage and trajectory of cancer in future studies.

Self-Oriented Empathy and Compassion Fatigue: The Serial Mediation of Dispositional Mindfulness and Counselor's Self-Efficacy.

This study aimed to explore the association between self-oriented empathy and compassion fatigue, and examine the potential mediating roles of dispositional mindfulness and the counselor's self-efficacy. A total of 712 hotline psychological counselors were recruited from the Mental Health Service Platform at Central China Normal University, Ministry of Education during the outbreak of Corona Virus Disease 2019, then were asked to complete the questionnaires measuring self-oriented empathy, compassion fatigue, dispositional mindfulness, and counselor's self-efficacy. Structural equation modeling was utilized to analyze the possible associations and explore potential mediations. In addition to reporting confidence intervals (CI), we employed a new method named model-based constrained optimization procedure to test hypotheses of indirect effects. Results showed that self-oriented empathy was positively associated with compassion fatigue. Dispositional mindfulness and counselor's self-efficacy independently and serially mediated the associations between self-oriented empathy and compassion fatigue. The findings of this study confirmed and complemented the etiological and the multi-factor model of compassion fatigue. Moreover, the results indicate that it is useful and necessary to add some training for increasing counselor's self-efficacy in mindfulness-based interventions in order to decrease compassion fatigue.

Structural Parameters Optimization of Elastic Cell in a Near-Bit Drilling Engineering Parameters Measurement Sub.

The downhole engineering parameters measurement sub is a key component of the rotary steerable drilling system. To enable a measurement sub to serve reliably under downhole complex conditions, the structural parameters optimization of its key but weak elastic cell is systematically studied. First, the multiple relations among measurement sensitivities, structural stiffnesses, and strength during structural parameters design are summarized. Second, the selection of the structural parameters of the elastic cell is characterized as a multi-objective optimization model, which is solved using the non-dominated sorting genetic algorithm II (NSGA-II). Furthermore, the finite element method (FEM) is used to verify the measurement performance and static strength of the proposed structure. Finally, transient dynamics analysis is applied to investigate the dynamic strength of the designed structure. The results show that the proposed parameters optimization strategy can quickly obtain the database for the structural parameters design of an elastic cell. The static analysis results based on the FEM further verify the effectiveness of the proposed method. Transient dynamic analysis also reveals the relative rigor of the proposed methodology framework to some extent. This work has practical significance for improving the drilling efficiency and reducing drilling risks. In addition, this proposed methodology has good extensibility.

Identification of a Novel NOG Missense Mutation in a Chinese Family With Symphalangism and Tarsal Coalitions.

BACKGROUND: Proximal symphalangism (SYM1) is a rare genetic bone disorder characterized by the fusion of proximal interphalangeal joints in the hands and feet. Genetic studies have identified two genes underlying SYM1 as the noggin (NOG) and the growth differentiation factor 5 (GDF5). CASE REPORT: In the present report, a 43-year-old gravida at 11 weeks of gestation was referred for evaluation of abnormal fusions of the joints. In the initial diagnosis, physical examination was undertaken. However, traditional radiological examination was not applied due to the need to protect the fetus, making diagnosis results inefficient to determine the exact disease affecting the proband. To acquire alternative clinical evidences, we conducted radiological examinations on two other affected family members. The radiological examination revealed that they carried the symphalangism accompanied with tarsal coalition, a very rare manifestation of SYM1. A combination of whole exome sequencing (WES) and Sanger sequencing revealed a novel heterozygous missense mutation (c.163G > T; p.Asp55Tyr) in the NOG gene, which could be associated with the observed pathogenic SYM1 in the studied family. The p.Asp55Tyr mutation co-segregated with SYM1 through the affected and unaffected family members. In silico structural modeling of the p.Asp55Tyr mutation showed that it abolishes the interaction with the Arg167 residue and causes a change in the electrostatic potential profile of the type II binding site of the noggin protein. CONCLUSION: Our findings indicate that the genetic test based on WES can be useful in diagnosing SYM1 patients, with particular advantages in preventing the fetus from contacting harmful X-ray through the traditional radiography. The novel pathogenic mutation identified would further expand our understanding of the mutation spectrum of NOG in association with SYM1 disease and provide a guidance on how to determine whether the fetus is affected by SYM1 through the prenatal diagnosis.

The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides.

MicroRNAs (miRNAs) are ribonucleic acids (RNAs) of ∼21 nucleotides that interfere with the translation of messenger RNAs (mRNAs) and play significant roles in development and diseases. In bilaterian animals, the specificity of miRNA targeting is determined by sequence complementarity involving the seed. However, the role of the remaining nucleotides (non-seed) is only vaguely defined, impacting negatively on our ability to efficiently use miRNAs exogenously to control gene expression. Here, using reporter assays, we deciphered the role of the base pairs formed between the non-seed region and target mRNA. We used molecular modeling to reveal that this mechanism corresponds to the formation of base pairs mediated by ordered motions of the miRNA-induced silencing complex. Subsequently, we developed an algorithm based on this distinctive recognition to predict from sequence the levels of mRNA downregulation with high accuracy (r2 > 0.5, P-value < 10-12). Overall, our discovery improves the design of miRNA-guide sequences used to simultaneously downregulate the expression of multiple predetermined target genes.