Miracle-dz/UniFAR-FTUs huggingface dataset:
Lattice Boltzmann Method for the Simulation of High Reynolds Number Flows

The lattice Boltzmann method (LBM) is considered as an alternative scheme to the standard Navier-Stokes approach. To simulate the high Reynolds number turbulence, several approaches based on LBM have been proposed. Among them, 5 approaches including the direct numerical simulation, dynamic subgrid scale model, inertial range consistent subgrid model, very large eddy simulation and entropic lattice Boltzmann method are discussed in detail. Features including improvements and shortcomings of each approach are presented. Whats more, application prospects of these approaches in high Reynolds number turbulence simulations are pointed out.
Cleo: A testbed for bridging model and experiment by simulating closed-loop stimulation, electrode recording, and optogenetics

Recent advances in neurotechnology enable exciting new experiments, including novel paradigms such as closed-loop optogenetic control that achieve powerful causal interventions. At the same time, improved computational models are capable of reproducing behavior and neural activity with increasing fidelity. However, the complexities of these advances can make it difficult to reap the benefits of bridging model and experiment, such as in-silico experiment prototyping or direct comparison of model output to experimental data. We can bridge this gap more effectively by incorporating the simulation of the experimental interface into our models, but no existing tool integrates optogenetics, electrode recording, and flexible closed-loop processing with neural population simulations. To address this need, we have developed the Closed-Loop, Electrophysiology, and Optogenetics experiment simulation testbed (Cleo). Cleo is a Python package built on the Brian 2 simulator enabling injection of recording and stimulation devices as well as closed-loop control with realistic latency into a spiking neural network model. Here we describe the design, features, and use of Cleo, including validation of the individual system components. We further demonstrate its utility in three case studies using a variety of existing models and discuss potential applications for advancing causal neuroscience.
DeepERA: deep learning enables comprehensive identification of drug-target interactions via embedding of heterogeneous data

Drug-target interaction prediction is a crucial step in drug development, discovery, and repurposing. Due to the tremendous combinatorial search space of all drug-protein pairs, machine learning algorithms have been utilized to facilitate the identification of novel drug-target interactions. Deep learning, known as a powerful learning system, has recently shown superior performance to traditional machine learning in many biological and biomedical areas. In this paper, we proposed an end-to-end deep learning model, DeepERA, to identify drug-target interactions based on heterogeneous data. This model assembles three independent feature embedding modules (intrinsic embedding, relational embedding, and annotation embedding) which each represent different attributes of the dataset and jointly contribute to the comprehensive predictions. This is the first work that, to our knowledge, applied deep learning models to learn each intrinsic features, relational features, and annotation features and combine them to predict drug-protein interactions. Our results showed that DeepERA outperformed other deep learning approaches proposed recently. The studies of individual embedding modules explained the dominance of DeepERA and confirmed the effects of the “guilt by associations” assumption on the performance of the prediction model. Using our DeepERA framework, we identified 45,603 novel drug-protein interactions for the whole human proteome, including 356 drug-protein interactions for the human proteins targeted by SARS-CoV-2 viral proteins. We also performed computational docking for the selected interactions and conducted a two-way statistical test to “normalize” the docking scores of different proteins/drugs to support our predictions.
Spraying alginate oligosaccharide improves photosynthetic performance and sugar accumulation in citrus by regulating antioxidant system and related gene expression

Alginate oligosaccharides (AOS) are functional substances in seaweed extracts that regulate crop quality and stress tolerance. In this paper, the effects of AOS spray application on the antioxidant system, photosynthesis and fruit sugar accumulation in citrus was investigated through a two-year field experiment. The results showed that 8-10 spray cycles of 300-500 mg L-1 AOS (once per 15 days) increased soluble sugar and soluble solid contents by 7.74-15.79% and 9.98-15.35%, respectively, from citrus fruit expansion to harvesting. Compared with the control, the antioxidant enzyme activity and the expression of some related genes in citrus leaves started to increase significantly after the 1st AOS spray application, while the net photosynthetic rate of leaves increased obviously only after the 3rd AOS spray cycle, and the soluble sugar content of AOS-treated leaves increased by 8.43-12.96% at harvest. This suggests that AOS may enhance photosynthesis and sugar accumulation in leaves by antioxidant system regulation. Moreover, analysis of fruit sugar metabolism showed that during the 3rd to 8th AOS spray cycles, AOS treatment increased the activity of enzymes related to sucrose synthesis (SPS, SSs), upregulated the expression of sucrose metabolism (CitSPS1, CitSPS2, SUS) and transport (SUC3, SUC4) genes, and promoted the accumulation of sucrose, glucose and fructose in fruits. Notably, the concentration of soluble sugars in citrus fruits was significantly reduced at all treatments with 40% reduction in leaves of the same branch, but the loss of soluble sugars in AOS-treated fruits (18.18%) was higher than that in the control treatment (14.10%). It showed that there was a positive effect of AOS application on leaf assimilation product transport and fruit sugar accumulation. In summary, AOS application may improve fruit sugar accumulation and quality by regulating the leaf antioxidant system, increasing the photosynthetic rate and assimilate product accumulation, and promoting sugar transfer from leaves to fruits. This study shows the potential application of AOS in the production of citrus fruits for sugar enhancement.
The efficacy and safety of epirubicin and cyclophosphamide combined with pyrotinib in neoadjuvant treatment for HER2-positive breast cancer: A real-world study

Purpose Long-term survival benefit of anthracyclines for human epidermal growth factor receptor 2 (HER2)-positive breast cancer is clear. In the neoadjuvant treatment, compared with the monoclonal antibody such as trastuzumab and pertuzumab, the clinical benefit of pyrotinib, a new small-molecule tyrosine kinase inhibitor (TKI), as the main anti-HER2 strategy currently requires more research to determine. Our real-world study is the first prospective observational study in China to evaluate the efficacy and safety of epirubicin (E) and cyclophosphamide (C) with pyrotinib as anti-HER2 therapy in the neoadjuvant setting of patients with stage II-III HER2-positive breast cancer. Methods From May 2019 to December 2021, 44 untreated patients with HER2-positive nonspecific invasive breast cancer who received 4 cycles of neoadjuvant EC with pyrotinib. The primary endpoint was pathological complete response (pCR) rate. Secondary endpoints included the overall clinical response, breast pathological complete response rate (bpCR), the rate of axillary lymph nodes pathological negativity and adverse events (AEs). Other objective indicators were the rate of surgical breast-conserving, the negative conversion ratios of tumor markers. Results Thirty-seven (84.1%) of 44 patients completed this neoadjuvant therapy, and 35 (79.5%) had surgery and were included in the primary endpoint assessment. The objective response rate (ORR) of 37 patients was 97.3%. Two patients reached clinical complete response, 34 obtained clinical partial response, 1 sustained stable disease, and no one had progressive disease. Eleven (31.4%) of 35 patients who had surgery achieved bpCR and the rate of axillary lymph nodes pathological negativity was 61.3%. The tpCR rate was 28.6% (95% CI: 12.8-44.3%). Safety was evaluated in all 44 patients. Thirty-nine (88.6%) had diarrhea, and 2 developed grade 3 diarrhea. Four (9.1%) patients had grade 4 leukopenia. All grade 3-4 AEs could be improved after symptomatic treatment. Conclusion The regimen of 4 cycles of EC combined with pyrotinib presented some feasibility in the neoadjuvant setting for HER2-positive breast cancer with manageable safety. New regimens with pyrotinib should be evaluated for higher pCR in future. Trial registration chictr.org Identifier: ChiCTR1900026061.
Prognostication of papillary thyroid microcarcinoma based on preoperative ultrasound

Background Diagnosis of papillary thyroid microcarcinoma, defined as papillary thyroid carcinoma measuring 1cm or less in greatest diameter, has increased with improvements in ultrasound technology and widespread familiarity and utilization. Given the indolent course of papillary thyroid carcinoma, active surveillance is considered an acceptable alternative to surgical resection for select patients. Candidacy for active surveillance is determined by a number of patient and tumor characteristics. Specifically, the location of the tumor within the thyroid gland plays one of the key roles in decision making. Here we evaluate characteristics of the primary tumor and distance to the thyroid capsule in association with locoregional metastases to help guide risk assessment. Methods Retrospective chart review of all thyroid surgeries performed by two surgeons at one medical center from 2014-2021 to evaluate characteristics of papillary thyroid microcarcinoma on preoperative ultrasound that are associated with locoregional metastatic disease. Results Our data show a sensitivity of 65% and specificity of 95% for identifying regional metastases in papillary thyroid microcarcinoma using preoperative ultrasound. We found no correlation between regional metastasis and size of tumor, distance to thyroid capsule or trachea, tumor contour, or presence of autoimmune thyroiditis. Nodules in the superior or midpole were associated with central or lateral neck metastases, whereas nodules in the isthmus or inferior pole were only associated with central neck metastases. Conclusions Active surveillance may be a reasonable option for even those papillary thyroid microcarcinomas adjacent to the thyroid capsule.
Sleeve gastrectomy decreases high-fat diet induced colonic pro-inflammatory status through the gut microbiota alterations

Background High-fat diet (HFD) induced obesity is characterized with chronic low-grade inflammation in various tissues and organs among which colon is the first to display pro-inflammatory features associated with alterations of the gut microbiota. Sleeve gastrectomy (SG) is currently one of the most effective treatments for obesity. Although studies reveal that SG results in decreased levels of inflammation in multiple tissues such as liver and adipose tissues, the effects of surgery on obesity related pro-inflammatory status in the colon and its relation to the microbial changes remain unknown. Methods To determine the effects of SG on the colonic pro-inflammatory condition and the gut microbiota, SG was performed on HFD-induced obese mice. To probe the causal relationship between alterations of the gut microbiota and improvements of pro-inflammatory status in the colon following SG, we applied broad-spectrum antibiotics cocktails on mice that received SG to disturb the gut microbial changes. The pro-inflammatory shifts in the colon were assessed based on morphology, macrophage infiltration and expressions of a variety of cytokine genes and tight junction protein genes. The gut microbiota alterations were analyzed using 16s rRNA sequencing. RNA sequencing of colon was conducted to further explore the role of the gut microbiota in amelioration of colonic pro-inflammation following SG at a transcriptional level. Results Although SG did not lead to pronounced changes of colonic morphology and macrophage infiltration in the colon, there were significant decreases in the expressions of several pro-inflammatory cytokines including interleukin-1β (IL-1β), IL-6, IL-18, and IL-23 as well as increased expressions of some tight junction proteins in the colon following SG, suggesting an improvement of pro-inflammatory status. This was accompanied by changing populations of the gut microbiota such as increased richness of Lactobacillus subspecies following SG. Importantly, oral administrations of broad-spectrum antibiotics to delete most intestinal bacteria abrogated surgical effects to relieve colonic pro-inflammation. This was further confirmed by transcriptional analysis of colon indicating that SG regulated inflammation related pathways in a manner that was gut microbiota relevant. Conclusion These results support that SG decreases obesity related colonic pro-inflammatory status through the gut microbial alterations.
High magnetoresistance in sputtered Permalloy thin films through growth on seed layers of (Ni/sub 0.81/Fe/sub 0.19/)/sub 1-x/Cr/sub x/

The use of thin (Ni/sub 0.81/Fe/sub 0.19/)/sub 1-x/Cr/sub x/ seed layer for obtaining high anisotropic magnetoresistance in Permalloy (Ni/sub 0.81/Fe/sub 0.19/) films is reported. The process yields a high /spl Delta/R/R of for example, 3.2% for 120-/spl Aring/-thick NiFe, without high-temperature deposition or annealing. X-ray diffraction shows that the NiFeCr seed layer causes the formation of large [111] textured grains in the Permalloy film, and that the interface between these two layers is quite smooth. These both increase the /spl Delta/R and reduce the resistance R in the film, which lead to the high /spl Delta/R/R. Also discussed is the enhanced /spl Delta/R/R and thermal stability trilayer magnetoresistive sensors using this NiFeCr instead of Ta as a spacer.
Cancer-associated fibroblasts: The chief architect in the tumor microenvironment

Stromal heterogeneity of tumor microenvironment (TME) plays a crucial role in malignancy and therapeutic resistance. Cancer-associated fibroblasts (CAFs) are one of the major players in tumor stroma. The heterogeneous sources of origin and subsequent impacts of crosstalk with breast cancer cells flaunt serious challenges before current therapies to cure triple-negative breast cancer (TNBC) and other cancers. The positive and reciprocal feedback of CAFs to induce cancer cells dictates their mutual synergy in establishing malignancy. Their substantial role in creating a tumor-promoting niche has reduced the efficacy of several anti-cancer treatments, including radiation, chemotherapy, immunotherapy, and endocrine therapy. Over the years, there has been an emphasis on understanding CAF-induced therapeutic resistance in order to enhance cancer therapy results. CAFs, in the majority of cases, employ crosstalk, stromal management, and other strategies to generate resilience in surrounding tumor cells. This emphasizes the significance of developing novel strategies that target particular tumor-promoting CAF subpopulations, which will improve treatment sensitivity and impede tumor growth. In this review, we discuss the current understanding of the origin and heterogeneity of CAFs, their role in tumor progression, and altering the tumor response to therapeutic agents in breast cancer. In addition, we also discuss the potential and possible approaches for CAF-mediated therapies.
Editorial: Triangle crosstalk: Gut microbiota, immune reaction and metabolism

COPYRIGHT © 2023 Chu, Luo, Han and Niu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Triangle crosstalk: Gut microbiota, immune reaction and metabolism
Comparative analysis of 84 chloroplast genomes of Tylosema esculentum reveals two distinct cytotypes

Tylosema esculentum (marama bean) is an important orphan legume from southern Africa that has long been considered to have the potential to be domesticated as a crop. The chloroplast genomes of 84 marama samples collected from various geographical locations in Namibia and Pretoria were compared in this study. The cp genomes were analyzed for diversity, including SNPs, indels, structural alterations, and heteroplasmy. The marama cp genomes ranged in length from 161,537 bp to 161,580 bp and contained the same sets of genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The genes rpoC2 and rpoB, and the intergenic spacers trnT-trnL and ndhG-ndhI were found to be more diverse than other regions of the marama plastome. 15 haplotypes were found to be divided into two groups, differing at 122 loci and at a 230 bp inversion. One type appears to have greater variability within the major genome present, and variations amongst individuals with this type of chloroplast genome seems to be distributed within specific geographic regions but with very limited sampling for some regions. However, deep sequencing has identified that within most of the individuals, both types of chloroplast genomes are present, albeit one is generally at a very low frequency. The inheritance of this complex of chloroplast genomes appears to be fairly constant, providing a conundrum of how the two genomes co-exist and are propagated through generations. The possible consequences for adaptation to the harsh environment in which T. esculentum survives are considered. The results pave the way for marama variety identification, as well as for understanding the origin and evolution of the bean.
Discussing sexuality with patients with neurological diseases: A survey among neurologists working in Saudi Arabia

Background Neurological diseases frequently affect sexual activity, and the resulting sexual dysfunction can cause much distress for patients. However, despite the importance of such complaints, neurologists frequently do not ask patients about their sexual symptoms or how their neurological illness and medications are affecting their sexual health. This study aimed to identify these difficulties as well as potential obstructions to conversations for addressing sexual dysfunction in patients with neurological diseases. Methods This cross-sectional study was performed by sending invitation letters and questionnaires to registered neurologists in Saudi Arabia. The questionnaire was constructed to determine the possibility of discussing sexual activities and function with patients with neurological diseases and the possible obstacles neurologists face in this regard. Statistical analyses were performed using the Statistical Package of Social Sciences (SPSS) program version 25, and p-values of <0.05 were considered statistically significant. Results A total of 258 of 750 neurologists (34.4%) returned the survey, of which 252 had completed the entire survey; therefore, their responses were considered suitable for further analysis. The majority of the respondents (63.1%) seldom discussed sexuality with their patients, more than half of the participants never discussed sexuality with female patients, and patients aged 60 years or older. The most commonly reported barriers were the lack of spontaneous communication by patients regarding their sexual problems (82.1%), insufficient consultation time (60.7%), and barriers based on language/culture/religion (53.6%). The majority of the respondents (61.9%) expressed the need for training on discussing sexuality as a measure that may enhance the discussion of sexual life with patients. Most of the respondents (92.9%) considered the patients responsible for bringing up problems in their sexual functioning during a patient interview. Conclusion Sexual dysfunction is rarely discussed with patients showing neurological diseases, particularly with female patients. This is due to the patient's inability to articulate their sexual problems freely as well as a lack of consultation time. Training on discussing sexuality may enhance the discussion of sexual life with patients.
Editorial: Understanding emotions using brain imaging and stimulation techniques

COPYRIGHT © 2023 Simmons and Strigo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Understanding emotions using brain imaging and stimulation techniques
Notch signaling, hypoxia, and cancer

Notch signaling is involved in cell fate determination and deregulated in human solid tumors. Hypoxia is an important feature in many solid tumors, which activates hypoxia-induced factors (HIFs) and their downstream targets to promote tumorigenesis and cancer development. Recently, HIFs have been shown to trigger the Notch signaling pathway in a variety of organisms and tissues. In this review, we focus on the pro- and anti-tumorigenic functions of Notch signaling and discuss the crosstalk between Notch signaling and cellular hypoxic response in cancer pathogenesis, including epithelia-mesenchymal transition, angiogenesis, and the maintenance of cancer stem cells. The pharmacological strategies targeting Notch signaling and hypoxia in cancer are also discussed in this review.
Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion

Introduction Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. Methods In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. Results Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. Discussion Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.