Characterization of network hierarchy reflects cell state specificity in genome organization.

Dynamic chromatin structure acts as the regulator of transcription program in crucial processes including cancer and cell development, but a unified framework for characterizing chromatin structural evolution remains to be established. Here, we performed graph inferences on Hi-C data sets and derived the chromatin contact networks. We discovered significant decreases in information transmission efficiencies in chromatin of colorectal cancer (CRC) and T-cell acute lymphoblastic leukemia (T-ALL) compared to corresponding normal controls through graph statistics. Using network embedding in the Poincaré disk, the hierarchy depths of chromatin from CRC and T-ALL patients were found to be significantly shallower compared to their normal controls. A reverse trend of change in chromatin structure was observed during early embryo development. We found tissue-specific conservation of hierarchy order in chromatin contact networks. Our findings reveal the top-down hierarchy of chromatin organization, which is significantly attenuated in cancer.

Rice BARENTSZ genes are required to maintain floral developmental stability against temperature fluctuations.

BARENTSZ (BTZ), a core component of the exon junction complex, regulates diverse developmental processes in animals. However, its evolutionary and developmental roles in plants remain elusive. Here, we revealed that three groups of paralogous BTZ genes existed in Poaceae, and Group 2 underwent loss-of-function mutations during evolution. They showed surprisingly low (~33%) sequence identities, implying functional divergence. Two genes retained in rice, OsBTZ1 and OsBTZ3, were edited; however, the resultant osbtz1 and osbtz3 mutants showed similar floral morphological and functional defects at a low frequency. When growing under low-temperature conditions, developmental abnormalities became pronounced, and new floral variations were induced. In particular, stamen and carpel functionality was impaired in these rice btz mutants. The double-gene mutant osbtz1/3 shared these floral defects with an increased frequency, which was further induced under low-temperature conditions. OsBTZs interacted with OsMADS7 and OsMADS8, and the floral expressions of the OsTGA10 and MADS-box genes were correlatively altered in these osbtz mutants and responded to low-temperature treatment. These novel findings demonstrate that two highly diverged OsBTZs are required to maintain floral developmental stability under low-temperature conditions, and play an integral role in male and female fertility, thus providing new insights into the indispensable roles of BTZ genes in plant development and adaptive evolution.

Genome-wide analysis and expression profiling of the HD-ZIP gene family in kiwifruit.

The homeodomain-leucine zipper (HD-Zip) gene family plays a pivotal role in plant development and stress responses. Nevertheless, a comprehensive characterization of the HD-Zip gene family in kiwifruit has been lacking. In this study, we have systematically identified 70 HD-Zip genes in the Actinidia chinensis (Ac) genome and 55 in the Actinidia eriantha (Ae) genome. These genes have been categorized into four subfamilies (HD-Zip I, II, III, and IV) through rigorous phylogenetic analysis. Analysis of synteny patterns and selection pressures has provided insights into how whole-genome duplication (WGD) or segmental may have contributed to the divergence in gene numbers between these two kiwifruit species, with duplicated gene pairs undergoing purifying selection. Furthermore, our study has unveiled tissue-specific expression patterns among kiwifruit HD-Zip genes, with some genes identified as key regulators of kiwifruit responses to bacterial canker disease and postharvest processes. These findings not only offer valuable insights into the evolutionary and functional characteristics of kiwifruit HD-Zips but also shed light on their potential roles in plant growth and development.

End Group Engineering for Constructing A-D-A Fused-Ring Photosensitizers with Balanced Phototheranostics Performance.

Phototheranostics continues to flourish in cancer treatment. Due to the competitive relationships between these photophysical processes of fluorescence emission, photothermal conversion, and photodynamic action, it is critical to balance them through subtle photosensitizer designs. Herein, it is provided a useful guideline for constructing A-D-A photosensitizers with superior phototheranostics performance. Various cyanoacetate group-modified end groups containing ester side chains of different length are designed to construct a series of A-D-A photosensitizers (F8CA1 ∼ F8CA4) to study the structure-property relationships. It is surprising to find that the photophysical properties of A-D-A photosensitizers can be precisely regulated by these tiny structural changes. The results reveal that the increase in the steric hindrance of ester side chains has positive impacts on their photothermal conversion capabilities, but adverse impacts on the fluorescence emission and photodynamic activities. Notably, these tiny structural changes lead to their different aggregation behavior. The molecule mechanisms are detailedly explained by theoretical calculations. Finally, F8CA2 nanoparticles with more balanced photophysical properties perform well in fluorescence imaging-guided photothermal and type I&II photodynamic synergistic cancer therapy, even under hypoxic conditions. Therefore, this work provides a novel practicable construction strategy for desired A-D-A photosensitizers.

Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies.

There are many contrasting results concerning the effectiveness of Test-Trace-Isolate (TTI) strategies in mitigating SARS-CoV-2 spread. To shed light on this debate, we developed a novel static-temporal multiplex network characterizing both the regular (static) and random (temporal) contact patterns of individuals and a SARS-CoV-2 transmission model calibrated with historical COVID-19 epidemiological data. We estimated that the TTI strategy alone could not control the disease spread: assuming R0 = 2.5, the infection attack rate would be reduced by 24.5%. Increased test capacity and improved contact trace efficiency only slightly improved the effectiveness of the TTI. We thus investigated the effectiveness of the TTI strategy when coupled with reactive social distancing policies. Limiting contacts on the temporal contact layer would be insufficient to control an epidemic and contacts on both layers would need to be limited simultaneously. For example, the infection attack rate would be reduced by 68.1% when the reactive distancing policy disconnects 30% and 50% of contacts on static and temporal layers, respectively. Our findings highlight that, to reduce the overall transmission, it is important to limit contacts regardless of their types in addition to identifying infected individuals through contact tracing, given the substantial proportion of asymptomatic and pre-symptomatic SARS-CoV-2 transmission.

Two-stage stratified designs with survival outcomes and adjustment for misclassification in predictive biomarkers.

Biomarker stratified clinical trial designs are versatile tools to assess biomarker clinical utility and address its relationship with clinical endpoints. Due to imperfect assays and/or classification rules, biomarker status is prone to errors. To account for biomarker misclassification, we consider a two-stage stratified design for survival outcomes with an adjustment for misclassification in predictive biomarkers. Compared to continuous and/or binary outcomes, the test statistics for survival outcomes with an adjustment for biomarker misclassification is much more complicated and needs to take special care. We propose to use the information from the observed biomarker status strata to construct adjusted log-rank statistics for true biomarker status strata. These adjusted log-rank statistics are then used to develop sequential tests for the global (composite) hypothesis and component-wise hypothesis. We discuss the power analysis with the control of the type-I error rate by using the correlations between the adjusted log-rank statistics within and between the design stages. Our method is illustrated with examples of the recent successful development of immunotherapy in nonsmall-cell lung cancer.

Development and validation of a prognostic model for 90-day survival in patients with alcohol-associated cirrhosis and acute decompensation.

BACKGROUND/PURPOSE: Patients with alcohol-associated cirrhosis and acute decompensation are considered critically ill and have a higher risk of short-term mortality. This study aimed to establish a nomogram to evaluate their 90-day survival and identify factors that affect disease progression. METHODS: We included patients from September 2008 to December 2016 (n = 387 in the derivation group) and from January 2017 to August 2020 (n = 157 in the validation group). LASSO regression and Cox multivariate risk regression were used to analyze the influencing factors of the 90-day mortality risk, and a nomogram was constructed. The performance of a model was analyzed based on the C-index, area under the receiver operating curve, calibration curve, and decision curve analysis. RESULTS: Total bilirubin >10 upper limit of normal, high-density lipoprotein cholesterol, lymphocyte and monocyte ratios ≤2.33, white blood cells, and hemoglobin were identified as independent risk factors affecting the 90-day mortality risk of patients and the nomogram was developed. A nomogram demonstrated excellent model predictive accuracy in both the derivation and validation cohorts (C-index: 0.976 and 0.945), which was better than other commonly used liver scoring models (p < 0.05). The nomogram also performed good calibration ability and more clinical net benefit. According to the nomogram score, patients were divided into high- and low-risk groups. Mortality was significantly higher in the high-risk group than in the low-risk group (p < 0.0001). CONCLUSION: The nomogram could accurately predict the 90-day mortality risk in patients with alcohol-associated cirrhosis and acute decompensation, helping to identify high-risk patients and personalize treatment at their first admission.

Regional consistency assessment in multiregional clinical trials.

Multiregional clinical trials (MRCTs) have become a favored strategy for new drug development. The accurate evaluation of treatment effects across different regions is crucial for interpreting the results of MRCTs. Consistency between regional and overall results ensures the extrapolability of the overall conclusions to individual regions. While numerous statistical methods have been proposed for consistency assessment, a notable proportion necessitate a substantial escalation in sample size, particularly in scenarios involving more than four regions within MRCTs. This, paradoxically, undermines the fundamental intent of MRCTs. In addition, standardized statistical criteria for concluding consistency are yet to be established. In this paper, we develop further consistency assessment approaches in the framework of two multivariate likelihood ratio test-based methods, namely mLRTa and mLRTb, wherein consistency is cast as the alternative and null hypotheses. Notably, our exploration unveils that qualitative methods such as the funnel approach and PMDA methods are special instances of mLRTa. Furthermore, our work underscores that these three qualitative methodologies roughly share the same level of assurance probability (AP). Intriguingly, when the number of regions in an MRCT surpasses five, even when the overall sample size guarantees a power of 90% or more and the true treatment effects remain uniform across regions, the AP remains below the 70% mark. Drawing from our meticulous examination of operational attributes, we recommend mLRTa with positive treatment effects in all regions in the alternative hypothesis with significance level 0.5 or mLRTb with all regional treatment effects being equal in the null and significance level of 0.2.

Generalizing Treatment Effect to a Target Population Without Individual Patient Data in a Real-World Setting.

The innovative use of real-world data (RWD) can answer questions that cannot be addressed using data from randomized clinical trials (RCTs). While the sponsors of RCTs have a central database containing all individual patient data (IPD) collected from trials, analysts of RWD face a challenge: regulations on patient privacy make access to IPD from all regions logistically prohibitive. In this research, we propose a double inverse probability weighting (DIPW) approach for the analysis sponsor to estimate the population average treatment effect (PATE) for a target population without the need to access IPD. One probability weighting is for achieving comparable distributions in confounders across treatment groups; another probability weighting is for generalizing the result from a subpopulation of patients who have data on the endpoint to the whole target population. The likelihood expressions for propensity scores and the DIPW estimator of the PATE can be written to only rely on regional summary statistics that do not require IPD. Our approach hinges upon the positivity and conditional independency assumptions, prerequisites to most RWD analysis approaches. Simulations are conducted to compare the performances of the proposed method against a modified meta-analysis and a regular meta-analysis.

A case study: Assessing the efficacy of the revised dosage regimen via prediction model for recurrent event rate using biomarker data.

In recently conducted phase III trials in a rare disease area, patients received monthly treatment at a high dose of the drug, which targets to lower a specific biomarker level, closely associated with the efficacy endpoint, to around 10% across patients. Although this high dose demonstrated strong efficacy, treatments were withheld due to the reports of serious adverse events. Dosing in these studies were later resumed at a reduced dosage which targets to lower the biomarker level to 15%-35% across patients. Two questions arose after this disruption. The first is whether the efficacy of this revised regimen as measured by the reduction in annualized event rate is adequate to support the continuation of the development and the second is whether the potential bias due to the loss of patients during this dosing gap process can be gauged. To address these questions, we built a prediction model that quantitatively characterizes biomarker vs. endpoint relationship and predicts efficacy at the 15%-35% range of the biomarker level using the available data from the original high dose. This model predicts favorable event rate in the target biomarker level and shows that the bias due to the loss of patients is limited. These results support the continued development of the revised regimen, however, given the limitation of the data available, this prediction is planned to be validated further when data under the revised regimen become available.

End Group Nonplanarization Enhances Phototherapy Efficacy of A-D-A Fused-Ring Photosensitizer for Tumor Phototherapy.

Enhancing the phototherapy efficacy of organic photosensitizers through molecular design is a fascinating but challenging task. Herein, we propose a simple design strategy to first realize the generation of superoxide anion radical (O2•-) by A-D-A fused-ring photosensitizers. Through replacing one cyano group of traditional end group with an ester group, we designed a novel nonplanar end group (A unit) to synthesize a novel A-D-A photosensitizer F8CA. In a comparison with its counterpart F8CN with the traditional end group, F8CA displays more loose packing and larger spin-orbit coupling constants. The F8CA nanoparticles showed higher photodynamic activities with the generation capability of singlet oxygen (1O2), hydroxyl radical (•OH), and O2•-, while F8CN nanoparticles could only generate 1O2 and •OH. In addition, F8CA nanoparticles still remain high photothermal conversion efficiency (61%). As a result, F8CA nanoparticles perform well in hypoxia-tolerant tumor phototherapy. This study brings an effective design thought for A-D-A photosensitizers.

Integrating Pillar[5]arene and BODIPY for a Supramolecular Nanoplatform To Achieve Synergistic Photodynamic Therapy and Chemotherapy.

BODIPY photosensitizers have been integrated with a hypoxia-activated prodrug to achieve synergistic photodynamic therapy (PDT) and chemotherapy. A novel BODIPY derivative BDP-CN was designed and synthesized. It had two cyano groups to make it complex well with a water-soluble pillar[5]arene. Their association constant was calculated to be (6.8±0.9)×106  M-1 . After self-assembly in water, regular spherical nanocarriers can be formed; these were used to encapsulate the hypoxia-activated prodrug tirapazamine (TPZ). BDP-CN displayed excellent photodynamic activity to complete PDT. In this process, O2 can be continuously consumed to activate TPZ to allow it to be converted to a benzotriazinyl (BTZ) radical with high cytotoxicity to complete chemotherapy. As a result, the formed nanoparticles showed excellent synergistic photodynamic therapy and chemotherapy efficacy. The synergistic therapy mechanism is discussed in detail.

Full-length transcriptome sequencing and transgenic tobacco revealed the key genes in the chlorogenic acid synthesis pathway of Sambucus chinensis L.

Chlorogenic acid is a key chemical in antioxidation and antisepsis. Sambucus chinensis L. is an herbaceous plant rich in chlorogenic acid and a potential genetic resource for breeding high-chlorogenic acid plants. However, there are few studies on the synthesis pathway of chlorogenic acid in S. chinensis. Our study found chlorogenic acid accumulation in S. chinensis to be organ-specific, higher in leaves and buds but lower in roots, stems and fruits. A total number of 546,844 CCS (circular consensus sequence), including 402,767 full-length nonchimeric (FLNC) and 39 annotated sequences related to the synthesis of chlorogenic acid, was obtained by single-molecule real-time sequencing technology (SMRT). qRT-PCR showed that a number of key genes involved in chlorogenic acid synthesis were differentially expressed in various tissues of S. chinensis. Transgenic tobacco revealed that ectopic expression of the HCT homologous gene HCT-45178 increased the content of chlorogenic acid. Our results should be the first report of full-length transcriptome data of S. chinensis, which help to understand the basis of chlorogenic acid synthesis and provide a novel strategy for breeding tobacco cultivars with higher levels of chlorogenic acid.

Effect of dietary concentrate level on digestibility of nutrients in each region of the gastrointestinal tract and rumen fermentation in goats.

This study evaluated the effects of high concentrate diets (HCD) on the rumen fermentation and the digestibility of nutrients in different sites of the gastrointestinal tract (GIT) in goats. Four goats were used in a crossover design. The goats were fitted with a ruminal cannula and flexible T-cannulae proximal duodenum and terminal ileum. Treatments were as follows: low concentrate group (LCG) and high concentrate group (HCG). Duodenal flow and forestomach digestibility of starch were significantly higher in the HCG than those in the LCG (p < 0.05); There was no significant difference in ileum flow and digestibility of starch in the small intestine, large intestine and total GIT (p > 0.05). The digestibility of crude protein (CP) in the forestomach was significantly higher in the HCG than in the LCG (p < 0.05); the flow of the duodenum and ileum of CP, and the CP digestibility of the small intestine, large intestine and total GIT were not significantly different between groups (p > 0.05). The duodenal and ileal flow of neutral detergent fiber (NDF), the NDF digestibility of the different segments and total GIT were not significantly different between groups (p > 0.05). Compared to the LCG, the ruminal pH of the HCG was significantly lower (p < 0.05). The HCG concentrations of microbial crude protein, ammonia nitrogen and isovaleric acid were significantly higher (p < 0.05) than the LCG. The foam strength, foam production and viscosity of the rumen fluid in the HCG were higher than the LCG (p < 0.01). These results showed that when the goats were fed with HCD, the digestibility of nutrients was not significantly impaired, but the risk of frothy rumen bloat increased. ImplicationsDue to a serious shortage of high-quality roughage in China, producers commonly used a high-concentrate diet in ruminants, which can improve animal production performance.Gastrointestinal digestive function plays a vital role in the absorption of nutrients and the healthy growth of animals.Therefore, this research evaluated the digestibility of various nutrients in different segments of the gastrointestinal tract (GIT) under HCD feeding by using three-site cannula goats as experimental animals.The results indicated that the GIT of goats could fully digest nutrients such as starch and protein under HCD feeding conditions.

Utilization of treatment effect on a surrogate endpoint for planning a study to evaluate treatment effect on a final endpoint.

To design a phase III study with a final endpoint and calculate the required sample size for the desired probability of success, we need a good estimate of the treatment effect on the endpoint. It is prudent to fully utilize all available information including the historical and phase II information of the treatment as well as external data of the other treatments. It is not uncommon that a phase II study may use a surrogate endpoint as the primary endpoint and has no or limited data for the final endpoint. On the other hand, external information from the other studies for the other treatments on the surrogate and final endpoints may be available to establish a relationship between the treatment effects on the two endpoints. Through this relationship, making full use of the surrogate information may enhance the estimate of the treatment effect on the final endpoint. In this research, we propose a bivariate Bayesian analysis approach to comprehensively deal with the problem. A dynamic borrowing approach is considered to regulate the amount of historical data and surrogate information borrowing based on the level of consistency. A much simpler frequentist method is also discussed. Simulations are conducted to compare the performances of different approaches. An example is used to illustrate the applications of the methods.

A generalized weighted combination test of treatment effect for clinical trials with a sequential parallel comparison design and binary endpoint.

To address the issue of a large placebo effect in certain therapeutic areas, rather than the application of the traditional gold standard parallel group placebo-controlled design, different versions of the sequential parallel comparison design have been advocated. In general, the design consists of two consecutive stages and three treatment groups. Stage 1 placebo nonresponders potentially form a prespecified patient subgroup for formal between-treatment comparison at the final analysis. In this research, a version of the design is considered for a binary endpoint. To fully utilize all available data, a generalized weighted combination test is proposed in case placebo has a relatively small effect for some of the study endpoints. The weighted combination of the test based on stage 1 data and the test based on stage 2 data of stage 1 placebo nonresponders suggested in the literature uses only a part of the study data and is a special case of this generalized weighted combination test. A multiple imputation approach is outlined for handling missing not at random data. Simulation is conducted to evaluate the performances of the methods and a data example is employed to illustrate the applications of the methods.

What is the role of aerosol transmission in SARS-Cov-2 Omicron spread in Shanghai?

The Omicron transmission has infected nearly 600,000 people in Shanghai from March 26 to May 31, 2022. Combined with different control measures taken by the government in different periods, a dynamic model was constructed to investigate the impact of medical resources, shelter hospitals and aerosol transmission generated by clustered nucleic acid testing on the spread of Omicron. The parameters of the model were estimated by least square method and MCMC method, and the accuracy of the model was verified by the cumulative number of asymptomatic infected persons and confirmed cases in Shanghai from March 26 to May 31, 2022. The result of numerical simulation demonstrated that the aerosol transmission figured prominently in the transmission of Omicron in Shanghai from March 28 to April 30. Without aerosol transmission, the number of asymptomatic subjects and symptomatic cases would be reduced to 130,000 and 11,730 by May 31, respectively. Without the expansion of shelter hospitals in the second phase, the final size of asymptomatic subjects and symptomatic cases might reach 23.2 million and 4.88 million by May 31, respectively. Our results also revealed that expanded vaccination played a vital role in controlling the spread of Omicron. However, even if the vaccination rate were 100%, the transmission of Omicron should not be completely blocked. Therefore, other control measures should be taken to curb the spread of Omicron, such as widespread antiviral therapies, enhanced testing and strict tracking quarantine measures. This perspective could be utilized as a reference for the transmission and prevention of Omicron in other large cities with a population of 10 million like Shanghai.

Quantifying human mixing patterns in Chinese provinces outside Hubei after the 2020 lockdown was lifted.

BACKGROUND: Contact patterns play a key role in the spread of respiratory infectious diseases in human populations. During the COVID-19 pandemic, the regular contact patterns of the population have been disrupted due to social distancing both imposed by the authorities and individual choices. Many studies have focused on age-mixing patterns before the COVID-19 pandemic, but they provide very little information about the mixing patterns in the COVID-19 era. In this study, we aim at quantifying human heterogeneous mixing patterns immediately after lockdowns implemented to contain COVID-19 spread in China were lifted. We also provide an illustrative example of how the collected mixing patterns can be used in a simulation study of SARS-CoV-2 transmission. METHODS AND RESULTS: In this work, a contact survey was conducted in Chinese provinces outside Hubei in March 2020, right after lockdowns were lifted. We then leveraged the estimated mixing patterns to calibrate a mathematical model of SARS-CoV-2 transmission. Study participants reported 2.3 contacts per day (IQR: 1.0-3.0) and the mean per-contact duration was 7.0 h (IQR: 1.0-10.0). No significant differences in average contact number and contact duration were observed between provinces, the number of recorded contacts did not show a clear trend by age, and most of the recorded contacts occurred with family members (about 78%). The simulation study highlights the importance of considering age-specific contact patterns to estimate the COVID-19 burden. CONCLUSIONS: Our findings suggest that, despite lockdowns were no longer in place at the time of the survey, people were still heavily limiting their contacts as compared to the pre-pandemic situation.

Reactive school closure weakens the network of social interactions and reduces the spread of influenza.

School-closure policies are considered one of the most promising nonpharmaceutical interventions for mitigating seasonal and pandemic influenza. However, their effectiveness is still debated, primarily due to the lack of empirical evidence about the behavior of the population during the implementation of the policy. Over the course of the 2015 to 2016 influenza season in Russia, we performed a diary-based contact survey to estimate the patterns of social interactions before and during the implementation of reactive school-closure strategies. We develop an innovative hybrid survey-modeling framework to estimate the time-varying network of human social interactions. By integrating this network with an infection transmission model, we reduce the uncertainty surrounding the impact of school-closure policies in mitigating the spread of influenza. When the school-closure policy is in place, we measure a significant reduction in the number of contacts made by students (14.2 vs. 6.5 contacts per day) and workers (11.2 vs. 8.7 contacts per day). This reduction is not offset by the measured increase in the number of contacts between students and nonhousehold relatives. Model simulations suggest that gradual reactive school-closure policies based on monitoring student absenteeism rates are capable of mitigating influenza spread. We estimate that without the implemented reactive strategies the attack rate of the 2015 to 2016 influenza season would have been 33% larger. Our study sheds light on the social mixing patterns of the population during the implementation of reactive school closures and provides key instruments for future cost-effectiveness analyses of school-closure policies.

Bivariate Bayesian hypothesis testing with missing data in components.

Multiple endpoints and historical data borrowing may be simultaneously incorporated for enhancing efficiency and speeding up the new drug development process in the pharmaceutical industry. O'Brien's test is a widely used weighted combination test for multiplicity adjustment on multiple endpoints to control the overall type error rate in a weak sense. In this research, a modification on the O'Brien's test more specifically on the weights is considered for a trial with two primary endpoints to potentially increase power. The method can handle missing data in the current study and in the prior derivation for dynamic historical data borrowing. Simulations are conducted to compare the performances of different methods. A data example is used to illustrate the applications of the methods.