Miracle-dz/UniFAR-FTUs huggingface dataset:
Charting spatial ligand-target activity using Renoir

The advancement of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics has made it possible to infer interactions amongst heterogeneous cells and their surrounding cellular environments. Existing methods assist in the analysis of ligand-receptor interactions by either adding spatial information to the currently available scRNA-seq data or utilizing spot-level or high-resolution spatial transcriptomics data. However, till date, there is a lack of methods capable of mapping ligand-target interactions across a spatial topology with specific cell type composition, with the potential to shed further light on the niche-specific relationship between ligands and their downstream targets. Here we present Renoir for charting the ligand-target activities across a spatial topology and delineating spatial communication niches harboring specific ligand-target activities and cell type composition. Renoir can also spatially map pathway-level aggregate activity of ligand-target gene sets and identify domain-specific activities between ligands and targets. We applied Renoir to three spatial datasets ranging from development to disease to demonstrate its effectiveness in inferring cellular niches with distinct ligand-target interactions, spatially mapping hallmark pathway activities, ranking ligand activity across spatial niches, and visualizing overall cell type-specific, ligand-target interactions in spatial niches.
Algorithm and Simulation of Time-Dependent Shortest Paths of Urban Traffic

A delay model of at traffic junctions and an algorithm of the Traffic Light Based Shortest Paths(TLBSP)were proposed,and Dijkstra's algorithm was improved also.The TLBSP algorithm can fit most traffic networks and traffic rules at present and can be calculated for each vehicle.The experimental results show that,the paths based on the TLBSP algorithm are more optimal than the path based on Distance Shortest Paths and TDSP with fixed delay.In addition,the algorithm can be applied to urban traffic navigation.It is beneficial to reasonable distribution of urban vehicle and alleviate urban traffic congestion.
A Study on the Uncertain Robust Control of Robot Based on Dynamic Observer

With parameter inaccuracies and bounded disturbances, a robust control scheme based on velocity observations was proposed for robot systems in which only the positions can be precisely measured. By the introduction of a compensation term in the design of the sliding mode observer that counteracts the effect of system deviations to the velocity reconstruction, the exponential observation error is converged to a bounded region. Using the Lyapunov direct method in designing the robust control laws based on the normal model and observed velocity, the closed-loop system satisfies the local uniform ultimate boundedness. The effectiveness of the proposed scheme is verified through simulation studies on a 2D of planar robot.
Cross-spectrally pure light, cross-spectrally pure fields and statistical similarity in electromagnetic fields

This paper describes the concept of cross-spectrally pure light, implications of statistical similarity of an optical field on its cross-spectral purity and cross-spectrally pure fields. First, the concept of cross-spectral purity of light is analysed in the space-frequency domain by taking into account the vectorial nature of the radiation, and the conditions and reduction formula are obtained. Then, by utilizing statistical similarity, the relationship between cross-spectral purity and spatial coherence is explored in the electromagnetic field. Last, the conditions for cross-spectrally pure fields are discussed, the polychromatic plane wave and the far field produced by a planar, secondary, stochastic electromagnetic source are studied as examples, and moreover, the relationship between cross-spectral purity and spatial coherence, which we have drawn, is verified during the study.
Sensitivity of PBL schemes of the WRF-ARW model in simulating the boundary layer flow parameters for its application to air pollution dispersion modeling over a tropical station

Mesoscale atmospheric circulations play an important role in the transport of air pollution and local air quality issues. The planetary boundary layer (PBL), the thermo-dynamical structure and the flow field play an important role in air pollution dispersion. Hence, the PBL parameters over Nagpur, India are simulated using the ARW v. 3.6. 1 mesoscale model. High-resolution simulations are conducted with triple nested domains having a horizontal resolution of 27, 9 and 3 km, as well as 27 vertical levels by using the 1 . 1o NCEP Final Analysis meteorological fields for initial and boundary conditions. Eight fair-weather days in winter and summer (January and April 2009) with no significant synoptic activity were chosen for the study. Sensitivity experiments of the ARW model were conducted with two non-local (Yonsei University [YSU], and Asymmetric Convective Model v. 2 [ACM2]) and three local turbulence kinetic energy (TKE) closure (Mellor-Yamada Nakanishi and Niino Level 2.5 PBL [MYNN2], Mellor-Yamada-Janjic [MYJ], and quasi-normal scale elimination [QNSE]) turbulence diffusion parameterizations, to study the evolution of PBL parameters and the thermodynamical structure during the study period. After validation of the simulated parameters with the available in-situ data, it was revealed that the non-local PBL scheme YSU, followed by local scheme MYNN2, could able to capture the characteristic variations of surface meteorological variables and the thermodynamical structure of the atmosphere. The present results suggest that the PBL schemes, namely YSU and MYNN2, performed better in representing the boundary-layer parameters and are useful for air pollution dispersion studies.
Two-dimensional near-surface seismic imaging with surface waves : alternative methodology for waveform inversion

High-resolution seismic imaging is essential to improve results of hydrocarbon exploration.Elastic waves propagate in the Earth as body and surface waves, the latter being the mostenergetic ones. Body waves are preferred for exploration seismic imaging while surfacewaves are usually considered to be noise. However, it has been recognised that the nearsurface can be characterised by analysing surface waves and that such result may improvethe outcome of body-wave processing. Currently, surface waves analysis leads to retrievelocal 1D property profiles.We propose a waveform-based inversion procedure to derive 2D velocity models fromsurface waves. This method consists of a misfit functional modification of classical FullWaveform Inversion and we call it windowed-Amplitude Waveform Inversion (w-AWI). Weshow that w-AWI is robust regarding the choice of initial velocity model. We apply w-AWI tosynthetic and real data obtaining encouraging near-surface imaging results
Coexistence of a novel STRN-ALK, NBEA-ALK double-fusion in an ovarian malignant mesothelioma patient: a case report and review

Primary ovarian mesothelioma (POM) is a rare malignant tumor with poor prognosis. Although anaplastic lymphoma kinase gene (ALK) double-fusion partners have been found in various tumors, it is rarely reported in mesothelioma. In this article, we describe the coexistence of a novel STRN-ALK, neurobeachin (NBEA)-ALK double-fusion in a patient with primary ovarian mesothelioma. A 30-year-old woman was found to have pelvic masses for more than a year. Color Doppler ultrasound showed mixed mass in the left ovary and multiple solid masses in the right ovary. the patient underwent laparoscopic surgery, including total hysterectomy, bilateral salpingo-oopherectomy, pelvic lymph node and abdominal aortic lymph node resection, omentum resection and abdominal focus resection. Pathologic examination revealed bilateral ovarian malignant mesothelioma and no evidence of malignancy in the resected bilateral round/broad ligaments, bilateral parametrial tissues, vaginal stump, bilateral fallopian tubes, pelvic and paraaortic lymph nodes. Immunohistochemistry showed that it was positive for Calretinin, VIM, WT1, PAX8, mesothelin, CK5/6, PCK, CK7, MLH1, PMS2, MSH2, MSH6, weakly positive for BAP1, while being negative for Napsin A, P504S, CEA, D2-40, GATA3. The sequencing analysis identified STRN-ALK (intron3:intron19) and NBEA-ALK (intron1:intron16) double-ALK fusion. To the best of our knowledge, this is the first report that a novel NBEA-ALK and EML4-ALK coexist in one patient with POM. The patient has completed 6 cycles of continuous chemotherapy and is in stable condition. Whether ALK inhibitors can bring promising benefits to POM patients in the future deserves further study.
Microbial community and soil enzyme activities driving microbial metabolic efficiency patterns in riparian soils of the Three Gorges Reservoir

Riparian zones represent important transitional areas between aquatic and terrestrial ecosystems. Microbial metabolic efficiency and soil enzyme activities are important indicators of carbon cycling in the riparian zones. However, how soil properties and microbial communities regulate the microbial metabolic efficiency in these critical zones remains unclear. Thus, microbial taxa, enzyme activities, and metabolic efficiency were conducted in the riparian zones of the Three Gorges Reservoir (TGR). Microbial carbon use efficiency and microbial biomass carbon had a significant increasing trend along the TGR (from upstream to downstream); indicating higher carbon stock in the downstream, microbial metabolic quotient (qCO2) showed the opposite trend. Microbial community and co-occurrence network analysis revealed that although bacterial and fungal communities showed significant differences in composition, this phenomenon was not found in the number of major modules. Soil enzyme activities were significant predictors of microbial metabolic efficiency along the different riparian zones of the TGR and were significantly influenced by microbial α-diversity. The bacterial taxa Desulfobacterota, Nitrospirota and the fungal taxa Calcarisporiellomycota, Rozellomycota showed a significant positive correlation with qCO2. The shifts in key microbial taxa unclassified_k_Fungi in the fungi module #3 are highlighted as essential factors regulating the microbial metabolic efficiency. Structural equation modeling results also revealed that soil enzyme activities had a highly significant negative effect on microbial metabolism efficiency (bacteria, path coefficient = −0.63; fungi, path coefficient = −0.67). This work has an important impact on the prediction of carbon cycling in aquatic-terrestrial ecotones. Graphical abstract
Evaluating the risk of knee osteoarthritis following unilateral ACL reconstruction based on an EMG-assisted method

Objective: Anterior cruciate ligament reconstruction (ACLR) cannot decrease the risk of knee osteoarthritis after anterior cruciate ligament rupture, and tibial contact force is associated with the development of knee osteoarthritis. The purpose of this study was to compare the difference in bilateral tibial contact force for patients with unilateral ACLR during walking and jogging based on an EMG-assisted method in order to evaluate the risk of knee osteoarthritis following unilateral ACLR. Methods: Seven unilateral ACLR patients participated in experiments. The 14-camera motion capture system, 3-Dimension force plate, and wireless EMG test system were used to collect the participants’ kinematics, kinetics, and EMG data during walking and jogging. A personalized neuromusculoskeletal model was established by combining scaling and calibration optimization. The inverse kinematics and inverse dynamics algorithms were used to calculate the joint angle and joint net moment. The EMG-assisted model was used to calculate the muscle force. On this basis, the contact force of the knee joint was analyzed, and the tibial contact force was obtained. The paired sample t-test was used to analyze the difference between the participants’ healthy and surgical sides of the participants. Results: During jogging, the peak tibial compression force on the healthy side was higher than on the surgical side (p = 0.039). At the peak moment of tibial compression force, the muscle force of the rectus femoris (p = 0.035) and vastus medialis (p = 0.036) on the healthy side was significantly higher than that on the surgical side; the knee flexion (p = 0.042) and ankle dorsiflexion (p = 0.046) angle on the healthy side was higher than that on the surgical side. There was no significant difference in the first (p = 0.122) and second (p = 0.445) peak tibial compression forces during walking between the healthy and surgical sides. Conclusion: Patients with unilateral ACLR showed smaller tibial compression force on the surgical side than on the healthy side during jogging. The main reason for this may be the insufficient exertion of the rectus femoris and vastus medialis.
Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage

Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars.
Case Report: Adjuvant image-guided radiation therapy reduces surgical invasiveness in malignant peripheral nerve sheath tumors

Introduction Malignant peripheral nerve sheath tumors (MPNSTs) are a group of rare soft tissue sarcomas of mesenchymal origin. These tumors generally require extensive local excision owing to their aggressive potential. Though the role of radiotherapy is controversial, in this report, we present the case of an MPNST in the forearm that was treated with microsurgery followed by image-guided radiation therapy to achieve complete tumor disappearance at the 18-month follow-up. Case report A 69-year-old woman with underlying paranoid schizophrenia was referred to our department with pain, severe swelling, and ecchymosis of her right forearm. Physical examination showed hypoesthesia in the segments innervated by the median nerve and reduced motor strength of her right hand. A gadolinium-enhanced MRI showed a large malignant peripheral nerve sheath tumor (13 x 8 x 7 cm) of the median nerve in the forearm. She underwent microsurgical en-bloc tumor resection with sparing of the median nerve. Thirty-five days postoperatively, she underwent image-guided radiotherapy (IGRT) using volumetric modulated arc therapy (VMAT). Serial MRI scans of the forearm with Gadolinium and whole-body CT scan with contrast enhancement at 30 days, 6 months, 1 year, and 18 months postoperatively documented no tumor recurrence, remnants, or metastases. Conclusions In this report, we demonstrate the successful use of advanced radiotherapy techniques such as IGRT while avoiding demolitive surgery for MPNST. Though a longer follow-up is necessary, at the 18-month follow-up, the patient demonstrated good outcomes from surgical resection followed by adjuvant RT for MPNST in the forearm.
Biological evaluation and in silico studies of novel compounds as potent TAAR1 agonists that could be used in schizophrenia treatment

Introduction: Schizophrenia is a serious mental illness that requires effective treatment with minimal adverse effects. As preclinical and clinical research progresses, trace amine-associated receptor 1 (TAAR1) is becoming a potential new target for the treatment of schizophrenia. Methods: We used molecular docking and molecular dynamics (MD) simulations to discover TAAR1 agonists. The agonistic or inhibitory effects of compounds on TAAR1, 5-HT1A, 5-HT2A, and dopamine D2-like receptors were determined. We used an MK801-induced schizophrenia-like behavior model to assess the potential antipsychotic effects of compounds. We also performed a catalepsy assay to detect the adverse effects. To evaluate the druggability of the compounds, we conducted evaluations of permeability and transporter substrates, liver microsomal stability in vitro, human ether-à-go-go-related gene (hERG), pharmacokinetics, and tissue distribution. Results: We discovered two TAAR1 agonists: compounds 50A and 50B. The latter had high TAAR1 agonistic activity but no agonistic effect on dopamine D2-like receptors and demonstrated superior inhibition of MK801-induced schizophrenia-like behavior in mice. Interestingly, 50B had favorable druggability and the ability to penetrate the blood-brain barrier (BBB) without causing extrapyramidal symptoms (EPS), such as catalepsy in mice. Conclusion: These results demonstrate the potential beneficial role of TAAR1 agonists in the treatment of schizophrenia. The discovery of a structurally novel TAAR1 agonist (50B) may provide valuable assistance in the development of new treatments for schizophrenia.
The potential impacts of climate change on ex situ conservation options for recalcitrant-seeded species

Recalcitrant seeds are characterized by desiccation and freezing sensitivity, and short storage longevity. These physiological attributes obviate their ex situ conservation in conventional seed banks, where seeds are stored dry at sub-zero temperatures (typically, 15% relative humidity and –20°C) for extended periods of time. Propagation of plants for field collections (e.g., botanical gardens, nurseries, and arboretums) is a valuable ex situ conservation option. However, these collections are relatively costly, require high maintenance, preserve limited genetic diversity and/or are directly exposed to biotic (e.g., pests) and abiotic (e.g., climatic) threats. Therefore, recalcitrant-seeded (RS) species are dependent on cryopreservation for their safe and long-term ex situ conservation. Different explant sources such as whole seeds, zygotic embryos, dormant buds, shoot tips, and pollen, can be used for plant propagation of RS species in field collections as well as for their cryopreservation. The success of the propagation or the cryopreservation of these explants often depends on their developmental status, vigor, and/or tolerance to desiccation and chilling/freezing. These attributes are modulated by the environment where the donor plant grows and we hypothesize that climate change, by affecting these biological attributes, would impact the success of explant propagation and cryopreservation. To support this hypothesis, we have reviewed how temperature changes and drought, the two main climate change scenarios, affect the main biological attributes that are directly involved in the success of ex situ conservation of tropical and temperate RS species. In general, increases in temperature and drought will negatively affect plant development in field collections and the quality of the explants used in cryopreservation. Consequently, field collections of RS species may need to be moved to more suitable places (e.g., higher latitudes/altitudes). Additionally, we may find a reduction in the success of cryopreservation of RS species germplasm directly harvested from field collections. However, we cannot always generalize these effects for all species since they often depend on the origin of the species (e.g., tropical and temperate species tend to respond to climate change differently), the genotype, the adaptive genetic potential of each population, and the severity of the environmental change. On the other hand, the increase in temperatures and water stress in donor plants at high-latitude areas and also some tropical environments may favor the production of seeds and seedlings better adapted to drying, and hence, increase the success of plant propagation and zygotic embryo cryopreservation.
Lower serum insulin-like growth factor 1 concentrations in patients with chronic insomnia disorder

Objectives Insulin-like growth factor 1 (IGF-1) is a crucial neurotrophin that is produced in the brain and periphery and may play an important role in insomnia and mood disorders. We aimed to analyze its serum concentrations in patients with chronic insomnia disorder (CID). Methods Patients with CID were enrolled in this study and divided into the CID group [Generalized Anxiety Disorder-7 (GAD-7) score < 10] and the CID with anxiety group (GAD-7 score ≥ 10). Age-and sex-matched healthy volunteers were recruited as controls. The Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep quality and the GAD-7 and the Patient Health Questionnaire-9 to assess emotional status. All subjects were monitored via polysomnography, and the serum IGF-1 concentrations in their peripheral blood were detected via enzyme-linked immunosorbent assays. Results We enrolled 65 patients with CID (of whom 35 had anxiety) and 36 controls. The PSQI score and IGF-1 concentration in the CID and CID with anxiety groups were higher than those in the control group. The apparent difference in IGF-1 concentration between the CID and CID with anxiety groups was not statistically significant. The IGF-1 concentration in patients with CID was linearly correlated with the GAD-7 score, PSQI score, and stage 3 non-rapid eye movement (stage N3) time. Conclusion The serum IGF-1 concentration in patients with CID was lower than that of participants without CID, negatively correlated with anxiety score and sleep quality, and positively correlated with stage N3 time.