Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering chloroplast development in rice through cell‐specific control of endogenous genetic circuits

Summary The engineering of C4 photosynthetic activity into the C3 plant rice has the potential to nearly double rice yields. To engineer a two‐cell photosynthetic system in rice, the rice bundle sheath (BS) must be rewired to enhance photosynthetic capacity. Here, we show that BS chloroplast biogenesis is enhanced when the transcriptional activator, Oryza sativa Cytokinin GATA transcription factor 1 (OsCGA1), is driven by a vascular specific promoter. Ectopic expression of OsCGA1 resulted in increased BS chloroplast planar area and increased expression of photosynthesis‐associated nuclear genes (PhANG), required for the biogenesis of photosynthetically active chloroplasts in BS cells of rice. A further refinement using a DNAse dead Cas9 (dCas9) activation module driven by the same cell‐type specific promoter, directed enhanced chloroplast development of the BS cells when gRNA sequences were delivered by the dCas9 module to the promoter of the endogenous OsCGA1 gene. Single gRNA expression was sufficient to mediate the transactivation of both the endogenous gene and a transgenic GUS reporter fused with OsCGA1 promoter. Our results illustrate the potential for tissue‐specific dCas9‐activation and the co‐regulation of genes needed for multistep engineering of C4 rice.
Magnetic resonance radiomics features and prognosticators in different molecular subtypes of pediatric Medulloblastoma

Purpose Medulloblastoma (MB) is a highly malignant pediatric brain tumor. In the latest classification, medulloblastoma is divided into four distinct groups: wingless (WNT), sonic hedgehog (SHH), Group 3, and Group 4. We analyzed the magnetic resonance imaging radiomics features to find the imaging surrogates of the 4 molecular subgroups of MB. Material and methods Frozen tissue, imaging data, and clinical data of 38 patients with medulloblastoma were included from Taipei Medical University Hospital and Taipei Veterans General Hospital. Molecular clustering was performed based on the gene expression level of 22 subgroup-specific signature genes. A total 253 magnetic resonance imaging radiomic features were generated from each subject for comparison between different molecular subgroups. Results Our cohort consisted of 7 (18.4%) patients with WNT medulloblastoma, 12 (31.6%) with SHH tumor, 8 (21.1%) with Group 3 tumor, and 11 (28.9%) with Group 4 tumor. 8 radiomics gray-level co-occurrence matrix texture (GLCM) features were significantly different between 4 molecular subgroups of MB. In addition, for tumors with higher values in a gray-level run length matrix feature—Short Run Low Gray-Level Emphasis, patients have shorter survival times than patients with low values of this feature (p = 0.04). The receiver operating characteristic analysis revealed optimal performance of the preliminary prediction model based on GLCM features for predicting WNT, Group 3, and Group 4 MB (area under the curve = 0.82, 0.72, and 0.78, respectively). Conclusion The preliminary result revealed that 8 contrast-enhanced T1-weighted imaging texture features were significantly different between 4 molecular subgroups of MB. Together with the prediction models, the radiomics features may provide suggestions for stratifying patients with MB into different risk groups.
Evaluation of Internet Gaming Disorder, Social Media Addiction, and Levels of Loneliness in Adolescents and Youth with Substance Use

Abstract Background and Objectives Substance use and addictive disorders are among the most significant public health concerns, particularly during adolescence. The current study aims to investigate internet gaming disorder, social media addiction, and loneliness levels in adolescents and youths with substance use. Methods: The study group consisted of 93 adolescents and youths aged 15–24 who presented to the Alcohol and Substance Addiction Research and Application Center or the Child and Adolescent Mental Health and Diseases outpatient clinic for substance use. Ninety-one healthy volunteers who did not use substances during any period of their lives participated as a control group. The participants fulfilled the Social Media Addiction Scale (SMAS), Internet Gaming Disorder Scale – Short-Form (IGDS9-SF), UCLA Loneliness Scale (UCLA-LS), and Drug Use Disorders Identification Test – Extended (DUDIT-E). Results: The symptoms of internet gaming disorder were significantly lower in the patient group compared with the control group. Although it was not significant, social media addiction was higher in the patient group than in the control group. The experience of loneliness was significantly higher in the patient group than in the control group. A significant negative correlation was found between treatment motivation and loneliness. Conclusions: School guidance teachers should monitor children who do not have friends or are lonely and be aware of the potential for substance use because it can emerge as a method of coping with the feeling of loneliness among adolescents. In future studies, investigating comprehensive factors contributing to different addictive behaviors may help to clarify the co-occurrence.
Systematic review and meta-analysis of psychological intervention on patients with coronary heart disease.

BACKGROUND Coronary heart disease is both a physical and mental disease, so psychological intervention can be used as part of a general cardiac rehabilitation plan. This study aimed to evaluate the effect of psychological intervention on the negative psychology of patients with coronary heart disease. METHODS Multiple databases like PubMed, Embase, Web of Science, and Cochrane Library were used to search for the relevant studies, and full-text articles involved in the evaluation of psychological intervention versus usual care for patients with coronary heart disease. Review Manager 5.4 (The Cochrane Collaboration, Software Update, Oxford, 2020) was adopted to estimate the effects of the results among selected articles. Forest plots, sensitivity analysis, and bias analysis were also performed on the included articles. RESULTS There were 17 studies that eventually met the final inclusion criteria. There were significant differences in anxiety level [mean difference (MD) -4.53; 95% confidence interval (CI), -6.36 to -2.7; P<0.00001; I2 =96%], depression level (MD-3.43; 95% CI, -4.85 to -2.01; P<0.00001; I2 =96%), and stress level (MD -4.19; 95% CI, -6.86 to -1.52; P<0.00001; I2 =94%), but no difference was found for total mortality (P=0.50). CONCLUSIONS This study indicated that psychological intervention has important health benefits for patients with coronary heart disease and can effectively reduce negative psychological effects such as depression, anxiety, and stress. However, the results need to be further confirmed due to the limitations.
Tree mycorrhizal type and tree diversity shape the forest soil microbiota.

There is limited knowledge on how the association of trees with different mycorrhizal types shapes soil microbial communities in the context of changing tree diversity levels. We used arbuscular (AM) and ectomycorrhizal (EcM) tree species as con- and heterospecific tree species pairs (TSPs), which were established in plots of three tree diversity levels including monocultures, two-species mixtures, and multi-tree species mixtures in a tree diversity experiment in subtropical China. We found that the tree mycorrhizal type had a significant effect on fungal but not bacterial alpha diversity. Furthermore, only EcM but not AM TSPs fungal alpha diversity increased with tree diversity, and the differences between AM and EcM TSPs disappeared in multi-species mixtures. Tree mycorrhizal type, tree diversity and their interaction had significant effects on fungal community composition. Neither fungi nor bacteria showed any significant compositional variation in TSPs located in multi-species mixtures. Accordingly, the most influential taxa driving the tree mycorrhizal differences at low tree diversity were not significant in multi-tree species mixtures. Collectively, our results indicate that tree mycorrhizal type is an important factor determining the diversity and community composition of soil microbes, and higher tree diversity levels promote convergence of the soil microbial communities. This article is protected by copyright. All rights reserved.
Effects of psychogenic stress on some peripheral and central inflammatory markers in rats with the different level of excitability of the nervous system

Patients with post-stress pathologies display the signs of inflammation in the peripheral blood as well as in the brain. The mechanisms of such post-stress neuroimmune changes, their contribution to the behavior, the relationship of the intensity of inflammation with genetically determined features have not been clarified. The goal of this work was to evaluate the dynamics of post-stress inflammation in the blood and hippocampus of rats which differ in level of excitability of the nervous system. Rats of two strains (high/low excitability threshold) were subjected to stress according to the K. Hecht protocol and their behavior, neutrophil:lymphocyte ratio and the number of Iba+ cells in the hippocampus were analysed 24 hours, 7 and 24 days after stress exposure. Highly excitable animals show an increase in anxiety-like behavior, in the number of neutrophils compared to lymphocytes as well as in the number of Iba1+ cells in CA1, CA3 and DG areas of the hippocampus in response to stress. Thus, hereditary high excitability of the nervous system is a possible risk factor for the development of post-stress pathologies.
High‐throughput dilution‐based growth method enables time‐resolved exo‐metabolomics of Pseudomonas putida and Pseudomonas aeruginosa

Understanding metabolism is fundamental to access and harness bacterial physiology. In most bacteria, nutrient utilization is hierarchically optimized according to their energetic potential and their availability in the environment to maximise growth rates. Low‐throughput methods have been largely used to characterize bacterial metabolic profiles. However, in‐depth analysis of large collections of strains across several conditions is challenging since high‐throughput approaches are still limited – especially for non‐traditional hosts. Here, we developed a high‐throughput dilution‐resolved cultivation method for metabolic footprinting of Pseudomonas putida and Pseudomonas aeruginosa. This method was benchmarked against a conventional low‐throughput time‐resolved cultivation approach using either a synthetic culture medium (where a single carbon source is present) for P. putida or a complex nutrient mixture for P. aeruginosa. Dynamic metabolic footprinting, either by sugar quantification or by targeted exo‐metabolomic analyses, revealed overlaps between the bacterial metabolic profiles irrespective of the cultivation strategy, suggesting a certain level of robustness and flexibility of the high‐throughput dilution‐resolved method. Cultivation of P. putida in microtiter plates imposed a metabolic constraint, dependent on oxygen availability, which altered the pattern of secreted metabolites at the level of sugar oxidation. Deep‐well plates, however, constituted an optimal cultivation set‐up yielding consistent and comparable metabolic profiles across conditions and strains. Altogether, the results illustrate the usefulness of this technological advance for high‐throughput analyses of bacterial metabolism for both biotechnological applications and automation purposes.
Parenchyma underlies the interspecific variation of xylem hydraulics and carbon storage across 15 woody species on a subtropical island in Japan.

Parenchyma is an important component of the secondary xylem. It has multiple functions and its fraction is known to vary substantially across angiosperm species. However, the physiological significance of this variation is not yet fully understood. Here, we examined how different types of parenchyma (ray and axial parenchyma, and axial parenchyma in direct contact with vessels [APV]) are coordinated with three essential xylem functions: water conduction, storage of non-structural carbohydrate (NSC), and mechanical support. Using branch sapwood of 15 co-occurring drought-adapted woody species from the subtropical Bonin Islands, Japan, we quantified ten xylem anatomical traits and examined their linkages to hydraulic properties, storage of soluble sugars and starch, and sapwood density. The fractions of APV and axial parenchyma in the xylem transverse sections were positively correlated with the percentage loss of conductivity in the native condition, whereas that of ray parenchyma was negatively correlated with the maximum conductivity across species. Axial and ray parenchyma fractions were positively associated with concentrations of starch and NSC. The fraction of parenchyma was independent of sapwood density, regardless of parenchyma type. We also identified a negative relationship between hydraulic conductivity and NSC storage and sapwood density, mirroring the negative relationship between the fractions of parenchyma and vessels. These results suggest that parenchyma fraction underlies species variation in xylem hydraulic and carbon use strategies, wherein xylem with a high fraction of axial parenchyma may adopt an embolism repair strategy through an increased starch storage with low cavitation resistance.
High‐Pressure CO Electroreduction at Silver Produces Ethanol and Propanol

Abstract Reducing CO2 to long‐chain carbon products is attractive considering such products are typically more valuable than shorter ones. However, the best electrocatalyst for making such products from CO2, copper, lacks selectivity. By studying alternate C2+ producing catalysts we can increase our mechanistic understanding, which is beneficial for improving catalyst performance. Therefore, we investigate CO reduction on silver, as density functional theory (DFT) results predict it to be good at forming ethanol. To address the current disagreement between DFT and experimental results (ethanol vs. no ethanol), we investigated CO reduction at higher surface coverage (by increasing pressure) to ascertain if desorption effects can explain the discrepancy. In terms of product trends, our results agree with the DFT‐proposed acetaldehyde‐like intermediate, yielding ethanol and propanol as C2+ products—making the CO2 electrochemistry of silver very similar to that of copper at sufficiently high coverage.
Long-term solid fuel use and risks of major eye diseases in China: A population-based cohort study of 486,532 adults

Background Over 3.5 billion individuals worldwide are exposed to household air pollution from solid fuel use. There is limited evidence from cohort studies on associations of solid fuel use with risks of major eye diseases, which cause substantial disease and economic burden globally. Methods and findings The China Kadoorie Biobank recruited 512,715 adults aged 30 to 79 years from 10 areas across China during 2004 to 2008. Cooking frequency and primary fuel types in the 3 most recent residences were assessed by a questionnaire. During median (IQR) 10.1 (9.2 to 11.1) years of follow-up, electronic linkages to national health insurance databases identified 4,877 incident conjunctiva disorders, 13,408 cataracts, 1,583 disorders of sclera, cornea, iris, and ciliary body (DSCIC), and 1,534 cases of glaucoma. Logistic regression yielded odds ratios (ORs) for each disease associated with long-term use of solid fuels (i.e., coal or wood) compared to clean fuels (i.e., gas or electricity) for cooking, with adjustment for age at baseline, birth cohort, sex, study area, education, occupation, alcohol intake, smoking, environmental tobacco smoke, cookstove ventilation, heating fuel exposure, body mass index, prevalent diabetes, self-reported general health, and length of recall period. After excluding participants with missing or unreliable exposure data, 486,532 participants (mean baseline age 52.0 [SD 10.7] years; 59.1% women) were analysed. Overall, 71% of participants cooked regularly throughout the recall period, of whom 48% used solid fuels consistently. Compared with clean fuel users, solid fuel users had adjusted ORs of 1.32 (1.07 to 1.37, p < 0.001) for conjunctiva disorders, 1.17 (1.08 to 1.26, p < 0.001) for cataracts, 1.35 (1.10 to 1.66, p = 0.0046) for DSCIC, and 0.95 (0.76 to 1.18, p = 0.62) for glaucoma. Switching from solid to clean fuels was associated with smaller elevated risks (over long-term clean fuel users) than nonswitching, with adjusted ORs of 1.21 (1.07 to 1.37, p < 0.001), 1.05 (0.98 to 1.12, p = 0.17), and 1.21 (0.97 to 1.50, p = 0.088) for conjunctiva disorders, cataracts, and DSCIC, respectively. The adjusted ORs for the eye diseases were broadly similar in solid fuel users regardless of ventilation status. The main limitations of this study include the lack of baseline eye disease assessment, the use of self-reported cooking frequency and fuel types for exposure assessment, the risk of bias from delayed diagnosis (particularly for cataracts), and potential residual confounding from unmeasured factors (e.g., sunlight exposure). Conclusions Among Chinese adults, long-term solid fuel use for cooking was associated with higher risks of not only conjunctiva disorders but also cataracts and other more severe eye diseases. Switching to clean fuels appeared to mitigate the risks, underscoring the global health importance of promoting universal access to clean fuels.
Combined Metabolically Active Tumor Volume and Early Metabolic Response Improve Outcome Prediction in Metastatic Colorectal Cancer

Visual Abstract Stratification of metastatic colorectal cancer (mCRC) patients is mostly based on clinical and biologic characteristics. This study aimed to validate the prognostic value of 18F-FDG PET/CT–based biomarkers such as baseline whole-body metabolically active tumor volume (WB-MATV) and early metabolic response (mR) in mCRC. Methods: The development cohort included chemorefractory mCRC patients enrolled in 2 prospective Belgian multicenter trials evaluating last-line treatments (multikinase inhibitors). The validation cohort included mCRC patients from an Italian center treated with chemotherapy and bevacizumab as first-line. Baseline WB-MATV was defined as the sum of metabolically active volumes of all target lesions identified on the baseline 18F-FDG PET/CT. Early mR assessment was performed following usual response criteria (response threshold of 30% [PERCIST–30%], response threshold of 15% [PERCIST–15%], European Organization for Research and Treatment of Cancer) and the so-called CONSIST method, which defines response as a decrease of SULmax ≥ 15% for all target lesions. Baseline WB-MATV and early mR assessment were investigated along with usual clinical factors and correlated with overall survival (OS) and progression-free survival (PFS). Results: Clinical factors, baseline WB-MATV, and early mR were evaluable in 192 of 239 and 94 of 125 patients of the development and validation cohorts, respectively. Except for PERCIST–30%, all response methods were equivalent in terms of outcome prediction, and CONSIST was found to be the most accurate. Baseline WB-MATV and early mR using the CONSIST method were independent prognostic parameters after adjustment for clinical factors in the development and validation sets for both OS (hazard ratio [HR] WB-MATV: 1.87 [95% CI, 1.17–2.97], P = 0.005, and HR early mR: 1.79 [95% CI, 1.08–2.95], P = 0.02 for the validation set) and PFS (HR WB-MATV: 1.94 [95% CI, 1.27–2.97], P = 0.002, and HR early mR: 1.69 [95% CI, 1.04–2.73], P = 0.03 for the validation set). Conclusion: Baseline WB-MATV and early mR are strong independent prognostic biomarkers for OS and PFS in mCRC, regardless of treatment received. Therefore, combining these biomarkers improves risk stratification for OS and PFS in mCRC.
A novel vision into the binding behavior of curcumin with human serum albumin-holo transferrin complex: molecular dynamic simulation and multi-spectroscopic perspectives

Abstract In this work, we investigated the simultaneous binding of curcumin (CUR) to human serum albumin (HSA) and human-holo transferrin (HTF) in the roles of binary and ternary systems. The binding affinity and binding site of protein-protein interaction were studied by the methods of multiple spectroscopic and molecular dynamics (MD) simulation. According to the results, the measurements for binding constant of HSA-CUR, HTF-CUR and (HSA-HTF) CUR complexes were observed to be 1.51 × 105, 7.93 × 104 and 1.44 × 105 M−1 respectively. Thermodynamic parameters were considered to be set at three varying temperatures including 298, 303, and 308 K. In conformity to the negative values of ΔH0 and ΔS0 the significant roles of hydrogen binding and van der-Waals forces in the formation of complexes are quiet evident. The binding distance between Trp residues of HSA, HTF and HSA-HTF upon interaction with CUR, were acquired by applying the Förster’s theory of non-radioactive energy transfer and reported to be 2.04 nm, 1.78 nm, and 1.86 nm, respectively. In accordance with the conductometry and Resonance light scattering (RLS) results, there were different interaction behaviors among the HSA-HTF complex and CUR in ternary system when being compared to the outcomes of binary system. The secondary structure of all three cases increased as the CUR concentration was intensified, which confirmed the inducement of proteins conformational changes through the application of circular dichroism (CD) technique. The experimental results that were acquired throughout the binding of HSA-CUR, HTF-CUR, and (HSA-HTF) CUR complexes were approved by molecular modeling. Communicated by Ramaswamy H. Sarma
Inclusion of photoautotrophic cultivated diatom biomass in salmon feed can deter lice

The aim of this study was to evaluate the potential of diatom (microalgae) biomass as a lice-reducing ingredient in salmon feed. The original hypothesis was based on the fact that polyunsaturated aldehydes (PUAs), e.g. 2-trans, 4-trans decadenial (A3) produced by diatoms can function as grazing deterrents and harm copepod development. Salmon lice (Lepeophtheirus salmonis) is a copepod, and we intended to test if inclusion of diatom biomass in the feed could reduce the infestation of lice on salmon. We performed experiments where salmon kept in tanks were offered four different diets, i.e. basic feed with diatoms, fish oil, Calanus sp. oil or rapeseed oil added. After a feeding period of 67 days a statistically representative group of fishes, tagged with diet group origin, were pooled in a 4000L tank and exposed to salmon lice copepodites whereafter lice infestation was enumerated. Salmon from all four diet groups had good growth with SGR values from 1.29 to 1.44% day-1 (increase from ca. 130 g to 350 g). At the termination of the experiment the number of lice on salmon offered diatom feed were statistically significantly lower than on salmon fed the other diets. Mean lice infestation values increased from diatom feed through Calanus and fish oil to standard feed with terrestrial plant ingredients. Analysis of the chemical composition of the different diets (fatty acids, amino acids) failed to explain the differences in lice infestation. The only notable result was that diatom and Calanus feed contained more FFA (free fatty acids) than feed with fish oil and the control feed. None of the potential deleterious targeted polyunsaturated aldehydes could be detected in skin samples of the salmon. What was exclusive for salmon that experienced reduced lice was diatom inclusion in the feed. This therefore still indicates the presence of some lice deterring ingredient, either in the feed, or an ingredient can have triggered production of an deterrent in the fish. An obvious follow up of this will be to perform experiments with different degrees of diatom inclusion in the feeds, i.e. dose response experiments combined with targeted PUA analyses, as well as to perform large scale experiments under natural conditions in aquaculture pens.