Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Genetic Structure of the Invasive Spotted Alfalfa Aphid Therioaphis trifolii (Hemiptera: Aphididae) in China Inferred From Complete Mitochondrial Genomes

Biological invasions represent a natural rapid evolutionary process in which invasive species may present a major threat to biodiversity and ecosystem integrity. Analyzing the genetic structure and demographic history of invaded populations is critical for the effective management of invasive species. The spotted alfalfa aphid (SAA) Therioaphis trifolii is indigenous in the Mediterranean region of Europe and Africa and has invaded China, causing severe damages to the alfalfa industry. However, little is known about its genetic structure and invasion history. In this study, we obtained 167 complete mitochondrial genome sequences from 23 SAA populations across China based on high-throughput sequencing and performed population genetic and phylogenomic analyses. High haplotype diversity and low nucleotide diversity were found in SAA populations in China with distinct genetic structures, i.e., all populations diverged into three phylogenetic lineages. Demographic history analyses showed a recent expansion of the SAA population, consistent with the recent invasion history. Our study indicated that SAA may have invaded through multiple introduction events during commercial trades of alfalfa, although this needs further validation by nuclear markers.
Association Between Patient Activation and Medication Adherence in Patients With Stroke: A Cross-Sectional Study

Background: Medication adherence is key to secondary prevention in patients with stroke. Poor medication adherence can lead to recurrence, disability, or even death in stroke survivors. Patient activation is associated with increased healthy behaviors and improved clinical outcomes in many chronic diseases. However, the association between patient activation and medication adherence in patients with stroke remains unclear. Objective: The study aimed to explore the influence of patient activation on the medication adherence of patients with stroke and to analyze the reasons for medication nonadherence. Materials and Methods: A cross-sectional design with convenience sampling was used in this study. A total of 119 patients with stroke were recruited from a tertiary hospital in Guangzhou. A social-demographic and clinical data form, a self-developed medication adherence questionnaire, and the 13-item Patient Activation Measure (PAM-13) were used. Univariate analysis and multiple linear regression analysis with dummy variables were conducted to investigate the associations between medication adherence and patient activation. Data were analyzed with IBM® SPSS® version 25.0. Results: The mean PAM-13 score in patients with stroke was 51.56 ± 12.58. A low level of patient activation was reported by up to 66.4% of the patients. The self-reported medication adherence questionnaire score was 5.59 ± 1.52. A low level of medication adherence was reported by up to 59.7% of the patients, while a moderate level was reported by 34.4%, and a high level was reported by only 5.9%. In the multiple stepwise regression analysis, patient activation was found to be an independent influencing factor of medication adherence in patients with stroke (p < 0.05). Conclusion: Medication adherence was poor in patients in Guangzhou, China, following an ischemic stroke. Patient activation as the independent influencing factor identified in this study will support healthcare givers to develop the tailored intervention to improve medication adherence among patients with stroke in China.
Drop-On-Demand Lubrication of Gears: A Feasibility Study

Different lubrication methods such as oil dip or injection lubrication are used in gearboxes to lubricate tribological contacts and to dissipate frictional heat. To improve resource and energy efficiency, novel needs-based lubrication methods like the drop-on-demand lubrication are being developed. It includes an ink-jet nozzle driven by a piezo element to generate picoliter droplets injected to tribological contacts. This study evaluates the feasibility of drop-on-demand lubrication of gears. Friction measurements in rolling-sliding contacts indicate the formation of typical elastohydrodynamic contacts. Power loss measurements of gears show a similar behavior compared to continuous minimum quantity lubrication. Hence, the study confirms that the operation of gears with drop-on-demand lubrication is possible. It introduces the possibility of dynamic and flexible oil supply on a contact needs-based level.
The Resistance Mechanisms and Treatment Strategies for ALK-Rearranged Non-Small Cell Lung Cancer

Anaplastic lymphoma kinase (ALK) is a validated molecular target for non-small-cell lung cancer (NSCLC). The use of tyrosine kinase inhibitors (TKIs) has led to significantly improved survival benefits. However, the clinical benefits of targeting ALK using TKIs are limited due to the emergence of drug resistance. The landscape of resistance mechanisms and treatment decisions has become increasingly complex. Therefore, continued research into new drugs and combinatorial therapies is required to improve outcomes in NSCLC. In this review, we explore the resistance mechanisms of ALK TKIs in advanced NSCLC in order to provide a theoretical basis and research ideas for solving the problem of ALK drug resistance.
Examining Differences in Fear Learning in Patients With Obsessive-Compulsive Disorder With Pupillometry, Startle Electromyography and Skin Conductance Responses

Obsessive-compulsive disorder (OCD) is characterized by recurrent, persistent thoughts and repetitive behaviors causing stress and anxiety. In the associative learning model of OCD, mechanisms of fear extinction are supposed to partly underlie symptom development, maintenance and treatment of OCD, proposing that OCD patients suffer from rigid memory associations and inhibitory learning deficits. To test these assumptions, previous studies have used skin conductance and subjective ratings as readouts in fear conditioning paradigms, finding impaired fear extinction learning, impaired fear extinction recall or no differences between individuals with OCD and healthy controls. Against this heterogeneous background, we tested fear acquisition and extinction in 37 OCD patients and 56 healthy controls, employing skin conductance as well as pupillometry and startle electromyography. Extinction recall was also included in a subsample. We did not observe differences between groups in any of the task phases, except a trend toward higher startle amplitudes during extinction for OCD. Overall, sensitive readouts such as pupillometry and startle responses did not provide evidence for moderate-to-large inhibitory learning deficits using classical fear conditioning, challenging the assumption of generically impaired extinction learning and memory in OCD.
Development and Verification of an Immune-Related Gene Pairs Prognostic Signature in Hepatocellular Carcinoma

With the increasing prevalence of Hepatocellular carcinoma (HCC) and the poor prognosis of immunotherapy, reliable immune-related gene pairs (IRGPs) prognostic signature is required for personalized management and treatment of patients. Gene expression profiles and clinical information of HCC patients were obtained from the TCGA and ICGC databases. The IRGPs are constructed using immune-related genes (IRGs) with large variations. The least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct IRGPs signature. The IRGPs signature was verified through the ICGC cohort. 1,309 IRGPs were constructed from 90 IRGs with high variability. We obtained 50 IRGPs that were significantly connected to the prognosis and constructed a signature that included 17 IRGPs. In the TCGA and ICGC cohorts, patients were divided into high and low-risk patients by the IRGPs signature. The overall survival time of low-risk patients is longer than that of high-risk patients. After adjustment for clinical and pathological factors, multivariate analysis showed that the IRGPs signature is an independent prognostic factor. The Receiver operating characteristic (ROC) curve confirmed the accuracy of the signature. Besides, gene set enrichment analysis (GSEA) revealed that the signature is related to immune biological processes, and the immune microenvironment status is distinct in different risk patients. The proposed IRGPs signature can effectively assess the overall survival of HCC, and provide the relationship between the signature and the reactivity of immune checkpoint therapy and the sensitivity of targeted drugs, thereby providing new ideas for the diagnosis and treatment of the disease.
Elasmobranch Responses to Experimental Warming, Acidification, and Oxygen Loss—A Meta-Analysis

Despite the long evolutionary history of this group, the challenges brought by the Anthropocene have been inflicting an extensive pressure over sharks and their relatives. Overexploitation has been driving a worldwide decline in elasmobranch populations, and rapid environmental change, triggered by anthropogenic activities, may further test this group's resilience. In this context, we searched the literature for peer-reviewed studies featuring a sustained (>24 h) and controlled exposure of elasmobranch species to warming, acidification, and/or deoxygenation: three of the most pressing symptoms of change in the ocean. In a standardized comparative framework, we conducted an array of mixed-model meta-analyses (based on 368 control-treatment contrasts from 53 studies) to evaluate the effects of these factors and their combination as experimental treatments. We further compared these effects across different attributes (lineages, climates, lifestyles, reproductive modes, and life stages) and assessed the direction of impact over a comprehensive set of biological responses (survival, development, growth, aerobic metabolism, anaerobic metabolism, oxygen transport, feeding, behavior, acid-base status, thermal tolerance, hypoxia tolerance, and cell stress). Based on the present findings, warming appears as the most influential factor, with clear directional effects, namely decreasing development time and increasing aerobic metabolism, feeding, and thermal tolerance. While warming influence was pervasive across attributes, acidification effects appear to be more context-specific, with no perceivable directional trends across biological responses apart from the necessary to achieve acid-base balance. Meanwhile, despite its potential for steep impacts, deoxygenation has been the most neglected factor, with data paucity ultimately precluding sound conclusions. Likewise, the implementation of multi-factor treatments has been mostly restricted to the combination of warming and acidification, with effects approximately matching those of warming. Despite considerable progress over recent years, research regarding the impact of these drivers on elasmobranchs lags behind other taxa, with more research required to disentangle many of the observed effects. Given the current levels of extinction risk and the quick pace of global change, it is further crucial that we integrate the knowledge accumulated through different scientific approaches into a holistic perspective to better understand how this group may fare in a changing ocean.
Dual Regulation of Tank Binding Kinase 1 by BRG1 in Hepatocytes Contributes to Reactive Oxygen Species Production

Excessive accumulation of reactive oxygen species (ROS) is considered a major culprit for the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We have previously shown that deletion of Brahma related gene 1 (BRG1) mitigated NAFLD in mice in part by attenuating ROS production in hepatocyte. Here we report that BRG1 deletion led to simultaneous down-regulation in expression and phosphorylation of tank binding kinase 1 (TBK1) in vivo and in vitro. On the one hand, BRG1 interacted with AP-1 to bind to the TBK1 promoter and directly activated TBK1 transcription in hepatocytes. On the other hand, BRG1 interacted with Sp1 to activate the transcription of c-SRC, a tyrosine kinase essential for TBK1 phosphorylation. Over-expression of c-SRC and TBK1 corrected the deficiency in ROS production in BRG1-null hepatocytes whereas depletion of TBK1 or c-SRC attenuated ROS production. In conclusion, our data suggest that dual regulation of TBK1 activity, at the transcription level and the post-transcriptional level, by BRG1 may constitute an important mechanism underlying excessive ROS production in hepatocytes.
Lulworthinone, a New Dimeric Naphthopyrone From a Marine Fungus in the Family Lulworthiaceae With Antibacterial Activity Against Clinical Methicillin-Resistant Staphylococcus aureus Isolates

The emergence of drug-resistant bacteria is increasing rapidly in all parts of the world, and the need for new antibiotics is urgent. In our continuous search for new antimicrobial molecules from under-investigated Arctic marine microorganisms, a marine fungus belonging to the family Lulworthiaceae (Lulworthiales, Sordariomycetes, and Ascomycota) was studied. The fungus was isolated from driftwood, cultivated in liquid medium, and studied for its potential for producing antibacterial compounds. Through bioactivity-guided isolation, a novel sulfated biarylic naphtho-α-pyrone dimer was isolated, and its structure was elucidated by spectroscopic methods, including 1D and 2D NMR and HRMS. The compound, named lulworthinone (1), showed antibacterial activity against reference strains of Staphylococcus aureus and Streptococcus agalactiae, as well as several clinical MRSA isolates with MICs in the 1.56–6.25 μg/ml range. The compound also had antiproliferative activity against human melanoma, hepatocellular carcinoma, and non-malignant lung fibroblast cell lines, with IC50 values of 15.5, 27, and 32 μg/ml, respectively. Inhibition of bacterial biofilm formation was observed, but no eradication of established biofilm could be detected. No antifungal activity was observed against Candida albicans. During the isolation of 1, the compound was observed to convert into a structural isomer, 2, under acidic conditions. As 1 and 2 have high structural similarity, NMR data acquired for 2 were used to aid in the structure elucidation of 1. To the best of our knowledge, lulworthinone (1) represents the first new bioactive secondary metabolite isolated from the marine fungal order Lulworthiales.
MRI-Derived Subcutaneous and Visceral Adipose Tissue Reference Values for Children Aged 6 to Under 18 Years

The assessment of body composition in pediatric population is essential for proper nutritional support during hospitalization. However, currently available methods have limitations. This study aims to propose a novel approach for nutrition status assessment and introduce magnetic resonance imaging (MRI)-derived subcutaneous and visceral fat normative reference values. A total of 262 healthy subjects aged from 6 to 18 years underwent MRI examinations and anthropometric measurements. MRI images at the second lumbar vertebrae were used by two radiologists to perform the semi-automatic tissue segmentation. Based on obtained adipose tissue surface areas and body mass index (BMI) scores sex-specific standard percentile curves (3rd, 10th, 25th, 50th, 75th, 90th, 97th) and z-scores were constructed using LMS method. Additionally, 85th and 95th centiles of subcutaneous and visceral adipose tissue were proposed as equivalents of overweight and obesity. Bland-Altman plots revealed an excellent intra-observer reproducibility and inter-observer agreement. In conclusion, our findings demonstrate highly reproducible method and suggest that MRI-derived reference values can be implemented in clinical practice.
Genome-Wide Analysis of the Phospholipase D Family in Five Cotton Species, and Potential Role of GhPLD2 in Fiber Development and Anther Dehiscence

Phospholipase D (PLD) and its hydrolysis product phosphatidic acid play an important role in the regulation of several cellular processes, including root growth, pollen tube elongation, and microtubule reorganization. Here, we systematically identified and analyzed the membership, characterization, and evolutionary relationship of PLDs in five species of cotton. The results of the transcriptomic analysis suggested that the evaluated PLD genes showed high expression levels in anther tissue and during the fiber initiation and elongation periods. Quantitative real-time polymerase chain reaction showed differential expression of GhPLD genes in the anthers of photoperiod sensitive male sterility mutant 5 (psm5). Previous research on multiple stable quantitative trait loci also suggests the role of PLD genes in the fiber development. Further analyses showed that GhPLD2 protein is localized to the plasma membrane. The virus-induced gene silencing of GhPLD2 in cotton seedlings repressed its expression by 40–70%, which led to a reduction in reactive oxygen species (ROS) levels, 22% anther indehiscence, and disrupted fiber initiation and elongation. Thus, we inferred that GhPLD2 may promote ROS production, which, in turn, may regulate anther dehiscence and fiber development.
Characterization of Exosome-Related Gene Risk Model to Evaluate the Tumor Immune Microenvironment and Predict Prognosis in Triple-Negative Breast Cancer

Background As a kind of small membrane vesicles, exosomes are secreted by most cell types from multivesicular endosomes, including tumor cells. The relationship between exosomes and immune response plays a vital role in the occurrence and development of tumors. Nevertheless, the interaction between exosomes and the microenvironment of tumors remains unclear. Therefore, we set out to study the influence of exosomes on the triple-negative breast cancer (TNBC) microenvironment. Method One hundred twenty-one exosome-related genes were downloaded from ExoBCD database, and IVL, CXCL13, and AP2S1 were final selected because of the association with TNBC prognosis. Based on the sum of the expression levels of these three genes, provided by The Cancer Genome Atlas (TCGA), and the regression coefficients, an exosome risk score model was established. With the median risk score value, the patients in the two databases were divided into high- and low-risk groups. R clusterProfiler package was employed to compare the different enrichment ways between the two groups. The ESTIMATE and CIBERSORT methods were employed to analyze ESTIMATE Score and immune cell infiltration. Finally, the correlation between the immune checkpoint-related gene expression levels and exosome-related risk was analyzed. The relationship between selected gene expression and drug sensitivity was also detected. Results Different risk groups exhibited distinct result of TNBC prognosis, with a higher survival rate in the low-risk group than in the high-risk group. The two groups were enriched by immune response and biological process pathways. A better overall survival (OS) was demonstrated in patients with high scores of immune and ESTIMATE rather than ones with low scores. Subsequently, we found that CD4+-activated memory T cells and M1 macrophages were both upregulated in the low-risk group, whereas M2 macrophages and activated mast cell were downregulated in the low-risk group in patients from the TCGA and GEO databases, respectively. Eventually, four genes previously proposed to be targets of immune checkpoint inhibitors were evaluated, resulting in the expression levels of CD274, CTLA4, LAG3, and TIM3 being higher in the low-risk group than high-risk group. Conclusion The results of our study suggest that exosome-related risk model was related to the prognosis and ratio of immune cell infiltration in patients with TNBC. This discovery may make contributions to improve immunotherapy for TNBC.
Insect and Disease Disturbances Correlate With Reduced Carbon Sequestration in Forests of the Contiguous United States

Major efforts are underway to harness the carbon sequestration capacity of forests to combat global climate change. However, tree damage and death associated with insect and disease disturbance can reduce this carbon sequestration capacity. We quantified average annual changes in live tree carbon accumulation associated with insect and disease disturbances utilizing the most recent (2001 – 2019) remeasurement data from National Forest Inventory plots in the contiguous United States. Forest plots recently impacted by insect disturbance sequestered on average 69% less carbon in live trees than plots with no recent disturbance, and plots recently impacted by disease disturbance sequestered on average 28% less carbon in live trees than plots with no recent disturbance. Nationally, we estimate that carbon sequestration by live trees, defined as the estimated average annual rate of above- and belowground carbon accumulation in live trees (diameter at breast height ≥ 2.54 cm) on forest land, has been reduced by 9.33 teragrams carbon per year (95% confidence interval: 7.11 to 11.58) in forests that have experienced recent insect disturbance and 3.49 teragrams carbon per year (95% confidence interval: 1.30 to 5.70) in forests that have experienced recent disease disturbance, for a total reduction of 12.83 teragrams carbon per year (95% confidence interval: 8.41 to 17.28). Strengthened international trade policies and phytosanitary standards as well as improved forest management have the potential to protect forests and their natural capacity to contribute to climate change mitigation.
Why Use Position Features in Liver Segmentation Performed by Convolutional Neural Network

Liver volumetry is an important tool in clinical practice. The calculation of liver volume is primarily based on Computed Tomography. Unfortunately, automatic segmentation algorithms based on handcrafted features tend to leak segmented objects into surrounding tissues like the heart or the spleen. Currently, convolutional neural networks are widely used in various applications of computer vision including image segmentation, while providing very promising results. In our work, we utilize robustly segmentable structures like the spine, body surface, and sagittal plane. They are used as key points for position estimation inside the body. The signed distance fields derived from these structures are calculated and used as an additional channel on the input of our convolutional neural network, to be more specific U-Net, which is widely used in medical image segmentation tasks. Our work shows that this additional position information improves the results of the segmentation. We test our approach in two experiments on two public datasets of Computed Tomography images. To evaluate the results, we use the Accuracy, the Hausdorff distance, and the Dice coefficient. Code is publicly available at: https://gitlab.com/hachaf/liver-segmentation.git.