Overlapping Indices for Dynamic Information Borrowing in Bayesian Hierarchical Modeling

Bayesian hierarchical model (BHM) has been widely used in synthesizing information across subgroups. Identifying heterogeneity in the data and determining proper strength of borrow have long been central goals pursued by researchers. Because these two goals are interconnected, we must consider them together. This joint consideration presents two fundamental challenges: (1) How can we balance the trade-off between homogeneity within the cluster and information gain through borrowing? (2) How can we determine the borrowing strength dynamically in different clusters? To tackle challenges, first, we develop a theoretical framework for heterogeneity identification and dynamic information borrowing in BHM. Then, we propose two novel overlapping indices: the overlapping clustering index (OCI) for identifying the optimal clustering result and the overlapping borrowing index (OBI) for assigning proper borrowing strength to clusters. By incorporating these indices, we develop a new method BHMOI (Bayesian hierarchical model with overlapping indices). BHMOI includes a novel weighted K-Means clustering algorithm by maximizing OCI to obtain optimal clustering results, and embedding OBI into BHM for dynamically borrowing within clusters. BHMOI can achieve efficient and robust information borrowing with desirable properties. Examples and simulation studies are provided to demonstrate the effectiveness of BHMOI in heterogeneity identification and dynamic information borrowing

Gaussian processes Correlated Bayesian Additive Regression Trees

In recent years, Bayesian Additive Regression Trees (BART) has garnered increased attention, leading to the development of various extensions for diverse applications. However, there has been limited exploration of its utility in analyzing correlated data. This paper introduces a novel extension of BART, named Correlated BART (CBART). Unlike the original BART with independent errors, CBART is specifically designed to handle correlated (dependent) errors. Additionally, we propose the integration of CBART with Gaussian processes (GP) to create a new model termed GP-CBART. This innovative model combines the strengths of the Gaussian processes and CBART, making it particularly well-suited for analyzing time series or spatial data. In the GP-CBART framework, CBART captures the nonlinearity in the mean regression (covariates) function, while the Gaussian processes adeptly models the correlation structure within the response. Additionally, given the high flexibility of both CBART and GP models, their combination may lead to identification issues. We provide methods to address these challenges. To demonstrate the effectiveness of CBART and GP-CBART, we present corresponding simulated and real-world examples

Strong plasmonic confinement and optical force in phosphorene pairs

The plasmonic responses in the spatially separated phosphorene (single-layer black phosphorus) pairs are investigated, mainly containing the field enhancement, light confinement, and optical force. It is found that the strong anisotropic dispersion of black phosphorus gives rise to the direction-dependent symmetric and anti-symmetric plasmonic modes. Our results demonstrate that the symmetrical modes possess stronger field enhancement, higher light confinement, and larger optical force than the anti-symmetric modes in the nanoscale structures. Especially, the light confinement ratio and optical force for the symmetric mode along the armchair direction of black phosphorus can reach as high as >90% and >3000 pN/mW, respectively. These results may open a new door for the light manipulation at nanoscale and the design of black phosphorus based photonic devices

The Long-Term Effects of Bariatric Surgery on Type 2 Diabetes Remission, Microvascular and Macrovascular Complications, and Mortality: a Systematic Review and Meta-Analysis.

This systematic review aimed to evaluate the long-term (≥ 5 years) outcomes of bariatric surgery on diabetes remission, microvascular and macrovascular events, and mortality among type 2 diabetes (T2D) patients. Ten articles (one randomized controlled trial and nine cohorts) met the inclusion criteria and were included in this review. Pooled estimates of nine cohort studies showed that surgery significantly increased the diabetes remission (relative risk (RR) = 5.90; 95% CI 3.75-9.28), reduced the microvascular (RR = 0.37; 95% CI = 0.30-0.46) and macrovascular events (RR = 0.52; 95% CI 0.44-0.61), and mortality (RR = 0.21; 95% CI 0.20-0.21) as compared to non-surgical treatment. Available evidence suggests better remission and lower risks of microvascular and macrovascular disease and mortality in the surgery group as compared to non-surgical treatment group in T2D patients after at least 5 years of follow-up

A Modeling Study of the Responses of Mesosphere and Lower Thermosphere Winds to Geomagnetic Storms at Middle Latitudes

Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model (TIMEGCM) simulations are diagnostically analyzed to investigate the causes of mesosphere and lower thermosphere (MLT) wind changes at middle latitudes during the 17 April 2002 storm. In the early phase of the storm, middle‐latitude upper thermospheric wind changes are greater and occur earlier than MLT wind changes. The horizontal wind changes cause downward vertical wind changes, which are transmitted to the MLT region. Adiabatic heating and heat advection associated with downward vertical winds cause MLT temperature increases. The pressure gradient produced by these temperature changes and the Coriolis force then drive strong equatorward meridional wind changes at night, which expand toward lower latitudes. Momentum advection is minor. As the storm evolves, the enhanced MLT temperatures produce upward vertical winds. These upward winds then lead to a decreased temperature, which alters the MLT horizontal wind pattern and causes poleward wind disturbances at higher latitudes

Поліморфізм качок породи shaoxing за мікросателітними локусами

Microsatellite markers are now been widely used for the detection and description of micropopulation processes occurring in the populations of domestic animals for the effects of various factors of breeding pressure. Microsatellite loci distributed throughout eukaryotic genomes, making them the preferred genetic marker for high resolution genetic mapping. In recent years, rapid advances have been made in the development of molecular genetic maps. High-density linkage maps are now available for many farm animals, such as cattle, pigs, and goats. In contrast, mapping studies in avian species are much less advanced except in the chicken. According to FAO about 70% of ducks are bred in China. This country is a leader in growing ducks. The Shaoxing breed is one of the three major duck breeds in China. Ducks of this breed are characterized by high performance. According to the Bureau of Product Quality, the age of maturity (the beginning of egg laying) in these birds occurs at 130–140 days. The characteristics of the Shaoxing breed include the fact that the peak period of laying eggs lasts from eight to ten months. On average, one duck in 500 days gives from 290 to 310 eggs, which is one of the highest rates for egg breeds. That is why the purpose of our study was the microsatellite analysis of two populations of Shaoxing breed with 9 locuses was conducted. The selection of birds for the study were carried out on a duck farms in Zhejiang Generation Biological Science and Technology Co., Ltd. and Zhuji Guowei Poultry Development Co, Ltd., and at the laboratory of the Jjejiang Academy of Sciences Institute. Samples collection and  DNA  preparation: Venous blood  samples  were  collected  from 480 ducks (240 ducks of population I and 240 ducks of population II of the Shaoxing breeds)  of  both populations  into  3  ml  tubes  containing  EDTA  as anticoagulant agent. In total of 9 investigated loci in the Shaoxing breed population, only one locus was monomorphic (SMO10). The number of different alleles (Na) for each polymorphic locus ranged from 2 (SMO12) to 13 (APL79, CMO11) in population I and from 2 (APL78, SMO12) to 7 (APL79) in population II. On average, one locus had 5.889 alleles in population I and 3.889 of alleles in the population II. The effective number of alleles (Nе) was 1.735 in population I and 1.599 in population II. The number of alleles and the expected heterozygosity (Hexp) values can provide important information for the discrimination of individuals and breeds. The index of expected heterozygosity in population I was 0.336 and 0.307 in population II. The information index (I) was 0,702 in population I and 0,576 in population II. For each population was found private alleles, in population I 6 alleles and in population II just 4 alleles. The results show high level of polymorphism of the studied populations of ducks. The obtained results can be used in the creation of new lines of ducks.У статті наведені результати досліджень генетичної структури двох популяцій качок породи шаосінь за використання дев’яти мікросателітних локусів. Птицю досліджували на качиних фермах компаній Zhejiang Generation Biological Science and Technology Co., Ltd. та Zhuji Guowei Poultry Development Co, Ltd. за підтримки лабораторії Poultry Genetics Laboratory of the Zhejiang Academy of Sciences (Zhejiang Province, PRC). Було встановлено, що середнє число ефективних алелів (Ne) на локус у популяції І складало 1,735, а для популяції ІІ – 1,599. Показники інформаційного індексу становили 0,702 (популяція І) та 0,576 (популяція ІІ). Фактична гетерозиготність у популяції І була 0,298, а у популяції ІІ – 0,269. У результаті нашого дослідження для кожної популяції були виявлені приватні алелі. З 9 досліджених локусів, у популяції І було виявлено 6 приватних алелів, в той час, коли популяція ІІ мала лише 4 локуси. Загалом у популяції І виявлено 23 приватних алелів, а у популяції ІІ – 5. Найбільша кількість приватних алелів була в локусі CMO11 (9), а найменша – 1 алель у локусі SMO7 та SMO10 в популяції І. Популяція ІІ була бідніша на приватні алелі, так у локусі APL79 було 2 та по 1 у CMO11, SMO7, SMO10. Отримані результати свідчать про високий рівень внутрішньопородного поліморфізму шаосінь, що дозволяє розробку стратегій збереження та використання генетичних ресурсів качки за використання аналізу поліморфних локусів мікросателіті

Efficacy and Clinicogenomic Correlates of Response to Immune Checkpoint Inhibitors Alone or With Chemotherapy in Non-Small Cell Lung Cancer

The role of combination chemotherapy with immune checkpoint inhibitors (ICI) (ICI-chemo) over ICI monotherapy (ICI-mono) in non-small cell lung cancer (NSCLC) remains underexplored. In this retrospective study of 1133 NSCLC patients, treatment with ICI-mono vs ICI-chemo associate with higher rates of early progression, but similar long-term progression-free and overall survival. Sequential vs concurrent ICI and chemotherapy have similar long-term survival, suggesting no synergism from combination therapy. Integrative modeling identified PD-L1, disease burden (Stage IVb; liver metastases), and STK11 and JAK2 alterations as features associate with a higher likelihood of early progression on ICI-mono. CDKN2A alterations associate with worse long-term outcomes in ICI-chemo patients. These results are validated in independent external (n = 89) and internal (n = 393) cohorts. This real-world study suggests that ICI-chemo may protect against early progression but does not influence overall survival, and nominates features that identify those patients at risk for early progression who may maximally benefit from ICI-chemo

Human Fetal Liver Stromal Cells That Overexpress bFGF Support Growth and Maintenance of Human Embryonic Stem Cells

In guiding hES cell technology toward the clinic, one key issue to be addressed is to culture and maintain hES cells much more safely and economically in large scale. In order to avoid using mouse embryonic fibroblasts (MEFs) we isolated human fetal liver stromal cells (hFLSCs) from 14 weeks human fetal liver as new human feeder cells. hFLSCs feeders could maintain hES cells for 15 passages (about 100 days). Basic fibroblast growth factor (bFGF) is known to play an important role in promoting self-renewal of human embryonic stem (hES) cells. So, we established transgenic hFLSCs that stably express bFGF by lentiviral vectors. These transgenic human feeder cells — bFGF-hFLSCs maintained the properties of H9 hES cells without supplementing with any exogenous growth factors. H9 hES cells culturing under these conditions maintained all hES cell features after prolonged culture, including the developmental potential to differentiate into representative tissues of all three embryonic germ layers, unlimited and undifferentiated proliferative ability, and maintenance of normal karyotype. Our results demonstrated that bFGF-hFLSCs feeder cells were central to establishing the signaling network among bFGF, insulin-like growth factor 2 (IGF-2), and transforming growth factor β (TGF-β), thereby providing the framework in which hES cells were instructed to self-renew or to differentiate. We also found that the conditioned medium of bFGF-hFLSCs could maintain the H9 hES cells under feeder-free conditions without supplementing with bFGF. Taken together, bFGF-hFLSCs had great potential as feeders for maintaining pluripotent hES cell lines more safely and economically