SynBa: improved estimation of drug combination synergies with uncertainty quantification.

MOTIVATION: There exists a range of different quantification frameworks to estimate the synergistic effect of drug combinations. The diversity and disagreement in estimates make it challenging to determine which combinations from a large drug screening should be proceeded with. Furthermore, the lack of accurate uncertainty quantification for those estimates precludes the choice of optimal drug combinations based on the most favourable synergistic effect. RESULTS: In this work, we propose SynBa, a flexible Bayesian approach to estimate the uncertainty of the synergistic efficacy and potency of drug combinations, so that actionable decisions can be derived from the model outputs. The actionability is enabled by incorporating the Hill equation into SynBa, so that the parameters representing the potency and the efficacy can be preserved. Existing knowledge may be conveniently inserted due to the flexibility of the prior, as shown by the empirical Beta prior defined for the normalized maximal inhibition. Through experiments on large combination screenings and comparison against benchmark methods, we show that SynBa provides improved accuracy of dose-response predictions and better-calibrated uncertainty estimation for the parameters and the predictions. AVAILABILITY AND IMPLEMENTATION: The code for SynBa is available at https://github.com/HaotingZhang1/SynBa. The datasets are publicly available (DOI of DREAM: 10.7303/syn4231880; DOI of the NCI-ALMANAC subset: 10.5281/zenodo.4135059).

An unusual sternalis with variation of the contralateral sternocleidomastoid muscle: a case report.

PURPOSE: To report a previously undocumented variant of sternalis. METHODS: An unusual muscle was observed during routine dissection. RESULTS: The sternalis muscle located in the right thoracic region originated from the superior portion of the rectus abdominis sheath and 5-6th costal cartilages, crossed the midline and attached at the sternum. The muscle fibers then ascended with the left sternocleidomastoid muscle as an additional fasciculus, of which the superior ends were finally terminated at the left mastoid process. The sternalis muscle of the thoracic region was innervated by the anterior cutaneous branches of right intercostal nerve, while the additional fasciculus ascended with the left sternocleidomastoid muscle was innervated by the branches of left accessory nerve. CONCLUSIONS: This study presents a unilateral sternalis muscle with the contralateral sternocleidomastoid variation. It will enhance the exhaustive classification of sternalis, and provide significant information to radiologists, angiologists and surgeons for better interpretation of images and safer interventions.

The pathology biopsy represents the "gold standard" for diagnosis: a case report.

A 70-year-old male with previously unknown immunodeficiency presented with multiple pulmonary nodular shadows observed on chest and abdomen radiography. Fungal infection was detected in brushing specimens, bronchial lavage, and transbronchial lung biopsy samples. Through next-generation sequencing (NGS) analysis, the patient was ultimately diagnosed with disseminated Talaromyces marneffei infection. Treatment with voriconazole at a dosage of 200 mg every 12 hours was initiated. However, after three months of treatment, the patient still had enlarged retroperitoneal lymph nodes, and a lymph node aspiration biopsy was performed to further clarify the diagnosis, which ultimately led to the diagnosis of Talaromyces marneffei infection and B-cell non-Hodgkin's lymphoma. The main significance of this study is to emphasize the importance for clinicians to obtain comprehensive specimens from patients presenting with multiple masses in order to ensure accurate clinical diagnosis.

E(n)-Equivariant cartesian tensor message passing interatomic potential.

Machine learning potential (MLP) has been a popular topic in recent years for its capability to replace expensive first-principles calculations in some large systems. Meanwhile, message passing networks have gained significant attention due to their remarkable accuracy, and a wave of message passing networks based on Cartesian coordinates has emerged. However, the information of the node in these models is usually limited to scalars, and vectors. In this work, we propose High-order Tensor message Passing interatomic Potential (HotPP), an E(n) equivariant message passing neural network that extends the node embedding and message to an arbitrary order tensor. By performing some basic equivariant operations, high order tensors can be coupled very simply and thus the model can make direct predictions of high-order tensors such as dipole moments and polarizabilities without any modifications. The tests in several datasets show that HotPP not only achieves high accuracy in predicting target properties, but also successfully performs tasks such as calculating phonon spectra, infrared spectra, and Raman spectra, demonstrating its potential as a tool for future research.

Group effects of desert rodent communities on plant seed dispersal.

Desert rodent communities spread plant seeds through the group effect of "selection complementation" and "fate complementation," which promotes the recovery of plant populations and the reconstruction of plant communities in desert areas.

Would future climate warming cause zoonotic diseases to spread over long distances?

Dipus sagitta is a major rodent found in arid environments and desert areas. They feed on plant seeds, young branches and some small insects, and have hibernating habits. Peak Dipus sagitta numbers impact the construction of the plant community in the environment, but also have a human impact as these rodents carry a variety of parasitic fleas capable of spreading serious diseases to humans. Based on 216 present distribution records of Dipus sagitta and seven environmental variables, this article simulates the potential distribution of Dipus sagitta during the Last Glacial Maximum, the mid-Holocene, the present and the future (2070s, RCP4.5, RCP8.5). This study also analyzes the geographic changes of the population distribution and evaluates the importance of climate factors by integrating contribution rate, replacement importance value and the jackknife test using the MaxEnt model. In this study, we opted to assess the predictive capabilities of our model using the receiver operating characteristic (ROC) and partial receiver operating characteristic (pROC) metrics. The findings indicate that the AUC value exceeds 0.9 and the AUC ratio is greater than 1, indicating superior predictive performance by the model. The results showed that the main climatic factors affecting the distribution of the three-toed jerboa were precipitation in the coldest quarter, temperature seasonality (standard deviation), and mean annual temperature. Under the two warming scenarios of the mid-Holocene and the future, there were differences in the changes in the distribution area of the three-toed jerboa. During the mid-Holocene, the suitable distribution area of the three-toed jerboa expanded, with a 93.91% increase in the rate of change compared to the Last Glacial Maximum. The size of the three-toed jerboa's habitat decreases under both future climate scenarios. Compared to the current period, under the RCP4.5 emission scenario, the change rate is -2.96%, and under the RCP8.5 emission scenario, the change rate is -7.41%. This indicates a trend of contraction in the south and expansion in the north. It is important to assess changes in the geographic population of Dipus sagitta due to climate change to formulate population control strategies of these harmful rodents and to prevent and control the long-distance transmission of zoonotic diseases.

Influence of biotic and abiotic factors on flea species population dynamics on Lasiopodomys brandtii.

Brandt's Vole (Lasiopodomys brandtii) is one of the most abundant rodent species in the grasslands of Inner Mongolia, China, and one of the main carriers of Yersinia pestis, the plague bacterium. There have been several instances of plague transmission among L. brandtii, and all of their dominant flea species are known carriers of plague. Little work has been done to understand the regulation of flea abundance on L. brandtii by biotic and abiotic factors. Here, we examine the impacts of host and climate variation on flea abundance on L. brandtii in May, July, and September of 2021 in the East Ujumqin Banner, Xilinhot City, Inner Mongolia Autonomous Region. We arrived at the following conclusions: 1) There were 8 flea species representing 2 families and 5 genera collected from L. brandtii, and Frontopsylla luculenta, Neopsylla pleskei orientalis, and Amphipsylla primaris mitis were most common. 2) Host body weight, host age, season, temperature, and humidity are key factors influencing flea abundance on L. brandtii. 3) Flea species vary in their respective responses to factors.

Controlling Effects of Nanocomposite Sterilant ND-1 on the Growth of Wild Populations of Midday Gerbil (Meriones meridianus).

Grassland is not only an important part of the terrestrial ecosystem with multiple ecological functions, but also an important base for Chinese herdsmen to produce and live. However, the occurrence and spread of rodent infestation reduces the biodiversity and productivity of grassland ecosystems. It also severely threatens human life, health, and biosecurity through disease transmission. In this study, we explored the ability of the nanocomposite sterilant ND-1 to control grassland rodent populations. Semi-closed experimental and control plots were established in the desert area of Alashan, Inner Mongolia, China. In spring 2018, the nanocomposite sterile ND-1 (Nongda-1) was introduced once, and the control effect of ND-1 on the growth of the wild population of midday gerbils was measured for two years. We show that ND-1 significantly reduced the population of midday gerbils in the experimental area, with a negative population growth rate. In addition, in the second year, the ratio of female midday gerbils to sub-adults in the experimental area was significantly lower than that in the control area, which resulted in a significant difference in the sex ratio of midday gerbils. There were significantly fewer females than males, and the population growth of midday gerbils in the experimental area was significantly inhibited. ND-1 had no significant effect on the home range of midday gerbils, and sterile individuals continued to occupy the home range and consume resources. Therefore, ND-1 reduced the number of female midday gerbils during the breeding period and the sex ratio and population density and altered the age structure of the wild population. Additionally, competition between sterile and normal individuals had a significant control effect on the growth of wild populations. Our studies demonstrate the significance of ND-1 in the sustainable control of grassland rodent pests, with the potential for limiting grassland rodent damage in the future.