Miracle-dz/UniFAR-FTUs huggingface dataset:
A Correlation Between Pericarpium Citri Reticulatae Volatile Components and the Change of the Coexisting Microbial Population Structure Caused by Environmental Factors During Aging

Pericarpium Citri Reticulatae (PCR) is a natural citrus by-product with beneficial health and nutritive properties that is used widely in food and is an ingredient in traditional Chinese medicine. PCR improves gradually with aging. However, the present research has not yet revealed the reasons for this. Some data prove the important role of microorganisms in the quality of tobacco and fermented tea with the time of the aging of these foods. Our studies further proved that the coexisting Aspergillus niger plays an important role in the change of flavonoids and volatile oil in PCR during this process. Therefore, we put forward that longer storage is better for PCR and is highly correlated with the change of the coexisting microbial population structure caused by environmental factors. Samples of PCR aged in Beijing, Sichuan, Guangdong, and Yunnan were collected at different time points. Using GC/MS and high throughput 16S rDNA and ITS sequencing techniques, massive changes in volatile profile and microbial communities were observed during aging. Spearman correlation analysis indicated that Exobasidium, Xeromyces, Pseudocercospora, Russula, Aspergillus, Herbaspirillum, Sphingomonas, and Streptococcus, which are the dominant microbial genera in Sichuan and Guangdong showed strong connections with volatile components of chemical markers. It was preliminarily verified that the changes of volatile components for PCR are highly correlated with the change of the coexisting microbial population structure caused by environmental factors, providing a new idea for the research on the aging mechanism of PCR and key influencing factors of aging quality.
Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow

Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.
Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
Periventricular white matter hyperintensities are associated with gait and balance in patients with minor stroke

Objective Cerebral small vessel disease (CSVD) is associated with gait and balance deficits in older adults. However, the effect of CSVD-related brain injury on post-stroke mobility is unknown. This study aimed to investigate the association of CSVD with gait and balance impairment after a minor stroke. Methods A total of 273 patients with a minor stroke (NIHSS ≤ 5 points) who were hospitalized at the Affiliated Hospital of Qingdao University were enrolled. The manifestations of white matter hyperintensities (WMH), lacunes, enlarged perivascular spaces (EPVS), and cerebral microbleeds (CMB) were statistically analyzed according to magnetic resonance imaging results, and the total burden score of CSVD was calculated. Gait function was assessed by a 6-m walking speed test, and balance function was assessed by the timed-up-and-go (TUG) test. Linear regression analysis was applied to determine the association after adjusting for key variables. Results The correlation results showed that in patients with minor stroke, age, sex, smoking history, and the infarct site were associated with gait speed, and age and the infarct site were associated with the TUG test. In the univariate linear regression model, periventricular white matter hyperintensities (PVWMH), deep white matter hyperintensities (DWMH), and the total burden of CSVD were correlated with gait speed, while only PVWMH correlated with the TUG test. After adjusting for confounders, only PVWMH were independent predictors of gait speed (β = −0.089, p < 0.05) and the TUG test (β = 0.517, p < 0.05). Conclusions Our study confirmed that CSVD is associated with gait and balance disorders after a minor stroke. PVWMH are independent predictors of gait and balance disorders in patients with minor stroke. These findings should be confirmed in larger prospective studies.
Efficacy and safety of intravenous acetaminophen (2 g/day) for reducing opioid consumption in Chinese adults after elective orthopedic surgery: A multicenter randomized controlled trial

Background: Acetaminophen is an important component of a multimodal analgesia strategy to reduce opioid consumption and pain intensity after an orthopedic surgery. The opioid-sparing efficacy of intravenous acetaminophen has been established at a daily dose of 4 g. However, it is still unclear for the daily dose of 2 g of acetaminophen, which is recommended by the China Food and Drug Administration Center for Drug Evaluation, in terms of its efficacy and safety. Objectives: This study aimed to evaluate the efficacy and safety of intravenous acetaminophen at a daily dose of 2 g for reducing opioid consumption and pain intensity after orthopedic surgery. Methods: In this multicenter, randomized, double-blind, placebo-controlled phase III trial, 235 patients who underwent orthopedic surgery were randomly assigned to receive intravenous acetaminophen 500 mg every 6 h or placebo. Postoperative morphine consumption, pain intensity at rest and during movement, and adverse events were analysed. Results: For the mean (standard deviation) morphine consumption within 24 h after surgery, intravenous acetaminophen was superior to placebo both in the modified intention-to-treat analysis [8.7 (7.7) mg vs. 11.2 (9.2) mg] in the acetaminophen group and the placebo group, respectively. Difference in means: 2.5 mg; 95% confidence interval, 0.25 to 4.61; p = 0.030), and in the per-protocol analysis (8.3 (7.0) mg and 11.7 (9.9) mg in the acetaminophen group and the placebo group, respectively. Difference in means: 3.4 mg; 95% confidence interval: 1.05 to 5.77; p = 0.005). The two groups did not differ significantly in terms of pain intensity and adverse events. Conclusion: Our results suggest that intravenous acetaminophen at a daily dose of 2 g can reduce morphine consumption by Chinese adults within the first 24 h after orthopedic surgery, but the extent of reduction is not clinically relevant. Clinical Trial Registration: [ClinicalTrials.gov], identifier [NCT02811991].
Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer

The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil. Graphical Abstract Dietary exposure to petroleum hydrocarbons and metals leads to changes in the gut microbiome and cytokine expression in Lates calcarifer.
Performance comparison of RGB and multispectral vegetation indices based on machine learning for estimating Hopea hainanensis SPAD values under different shade conditions

Reasonable cultivation is an important part of the protection work of endangered species. The timely and nondestructive monitoring of chlorophyll can provide a basis for the accurate management and intelligent development of cultivation. The image analysis method has been applied in the nutrient estimation of many economic crops, but information on endangered tree species is seldom reported. Moreover, shade control, as the common seedling management measure, has a significant impact on chlorophyll, but shade levels are rarely discussed in chlorophyll estimation and are used as variables to improve model accuracy. In this study, 2-year-old seedlings of tropical and endangered Hopea hainanensis were taken as the research object, and the SPAD value was used to represent the relative chlorophyll content. Based on the performance comparison of RGB and multispectral (MS) images using different algorithms, a low-cost SPAD estimation method combined with a machine learning algorithm that is adaptable to different shade conditions was proposed. The SPAD values changed significantly at different shade levels (p < 0.01), and 50% shade in the orthographic direction was conducive to chlorophyll accumulation in seedling leaves. The coefficient of determination (R2), root mean square error (RMSE), and average absolute percent error (MAPE) were used as indicators, and the models with dummy variables or random effects of shade greatly improved the goodness of fit, allowing better adaption to monitoring under different shade conditions. Most of the RGB and MS vegetation indices (VIs) were significantly correlated with the SPAD values, but some VIs exhibited multicollinearity (variance inflation factor (VIF) > 10). Among RGB VIs, RGRI had the strongest correlation, but multiple VIs filtered by the Lasso algorithm had a stronger ability to interpret the SPAD data, and there was no multicollinearity (VIF < 10). A comparison of the use of multiple VIs to estimate SPAD indicated that Random forest (RF) had the highest fitting ability, followed by Support vector regression (SVR), linear mixed effect model (LMM), and ordinary least squares regression (OLR). In addition, the performance of MS VIs was superior to that of RGB VIs. The R2 of the optimal model reached 0.9389 for the modeling samples and 0.8013 for the test samples. These findings reinforce the effectiveness of using VIs to estimate the SPAD value of H. hainanensis under different shade conditions based on machine learning and provide a reference for the selection of image data sources.
Intra and inter: Alterations in functional brain resting-state networks in patients with functional constipation

Background Functional constipation (FCon), is a symptom-based functional gastrointestinal disorder without an organic etiology and altering brain structure and function. However, previous studies mainly focused on isolated brain regions involved in brain plasticity. Therefore, little is known about the altered large-scale interaction of brain networks in FCon. Methods For this study, we recruited 20 patients with FCon and 20 healthy controls. We used group independent component analysis to identify resting-state networks (RSNs) and documented intra- and inter-network alterations in the RSNs of the patients with FCon. Results We found 14 independent RSNs. Differences in the intra-networks included decreased activities in the bilateral caudate of RSN 3 (strongly related to emotional and autonomic processes) and decreased activities in the left precuneus of RSN 10 (default mode network). Notably, the patients with FCon exhibited significantly decreased interactive connectivity between RSNs, mostly involving the connections to the visual perception network (RSN 7–9). Conclusion Compared with healthy controls, patients with FCon had extensive brain plastic changes within and across related RSNs. Furthermore, the macroscopic brain alterations in FCon were associated with interoceptive abilities, emotion processing, and sensorimotor control. These insights could therefore lead to the development of new treatment strategies for FCon.
Horses wait for more and better rewards in a delay of gratification paradigm

Self-control, defined as the ability to forgo immediate satisfaction in favor of better pay-offs in the future, has been extensively studied, revealing enormous variation between and within species. Horses are interesting in this regard because as a grazing species they are expected to show low self-control whereas its social complexity might be linked to high self-control abilities. Additionally, self-control may be a key factor in training and/or coping with potentially stressful husbandry conditions. We assessed horses’ self-control abilities in a simplified delay of gratification test that can be easily implemented in a farm setting. In Experiment 1, we gave horses (N = 52) the choice between an immediately available low-quality reward and a delayed high-quality reward that could only be obtained if the horse refrained from consuming the immediate reward. Different experimenters (N = 30) that underwent prior training in the procedures, tested horses in two test phases either with their eyes visible or invisible (sunglasses). Twenty horses waited up to the maximum delay stage of 60 s while all horses performed worse in the second test phase. In Experiment 2, we improved the test procedure (i.e., one experimenter, refined criterion for success), and tested 30 additional horses in a quality and quantity condition (one reward vs. delayed bigger reward). Two horses successfully waited for 60 s (quality: N = 1, quantity: N = 1). Horses tolerated higher delays, if they were first tested in the quantity condition. Furthermore, horses that were fed hay ad libitum, instead of in a restricted manner, reached higher delays. Coping behaviors (e.g., looking away, head movements, pawing, and increasing distance to reward) facilitated waiting success and horses were able to anticipate the upcoming delay duration as indicated by non-random distributions of giving-up times. We found no correlations between owner-assessed traits (e.g., trainability and patience) and individual performance in the test. These results suggest that horses are able to exert self-control in a delay of gratification paradigm similar to other domesticated species. Our simplified paradigm could be used to gather large scale data, e.g., to investigate the role of self-control in trainability or success in equestrian sports.
An Intelligent Rice Yield Trait Evaluation System Based on Threshed Panicle Compensation

High-throughput phenotyping of yield-related traits is meaningful and necessary for rice breeding and genetic study. The conventional method for rice yield-related trait evaluation faces the problems of rice threshing difficulties, measurement process complexity, and low efficiency. To solve these problems, a novel intelligent system, which includes an integrated threshing unit, grain conveyor-imaging units, threshed panicle conveyor-imaging unit, and specialized image analysis software has been proposed to achieve rice yield trait evaluation with high throughput and high accuracy. To improve the threshed panicle detection accuracy, the Region of Interest Align, Convolution Batch normalization activation with Leaky Relu module, Squeeze-and-Excitation unit, and optimal anchor size have been adopted to optimize the Faster-RCNN architecture, termed ‘TPanicle-RCNN,’ and the new model achieved F1 score 0.929 with an increase of 0.044, which was robust to indica and japonica varieties. Additionally, AI cloud computing was adopted, which dramatically reduced the system cost and improved flexibility. To evaluate the system accuracy and efficiency, 504 panicle samples were tested, and the total spikelet measurement error decreased from 11.44 to 2.99% with threshed panicle compensation. The average measuring efficiency was approximately 40 s per sample, which was approximately twenty times more efficient than manual measurement. In this study, an automatic and intelligent system for rice yield-related trait evaluation was developed, which would provide an efficient and reliable tool for rice breeding and genetic research.
Changes and Correlation Between Physiological Characteristics of Rhododendron simsii and Soil Microbial Communities Under Heat Stress

The relationship between Rhododendron simsii and its soil microbial community under heat stress was not clear. In this study, the effects of heat stress on the physiological characteristics, soil physicochemical properties and soil microbial community structure of R. simsii were investigated. The experimental control (CK) was set as day/night (14/10 h) 25/20°C and experimental treatments were set as light heat stress (LHS) 35/30°C and high heat stress (HHS) 40/35°C. Our results showed that, compared with CK, LHS treatment significantly increased malondialdehyde, hydrogen peroxide, proline and soluble sugar contents, as well as catalase and peroxidase activities, while HHS treatment significantly increased ascorbate peroxidase activity and decreased chlorophyll content. Compared with CK, LHS treatment significantly reduced soil ammonium-nitrogen and nitrate-nitrogen content, while HHS significantly increased soil ammonium-nitrogen content. Compared with CK, both treatments changed the soil microbial community structure. For bacterial community, LHS and HHS treatment resulting in the significant enrichment of Burkholderia-Caballeronia-Paraburkholderia and Occallatibacte, respectively. For fungal community, LHS treatment resulting in the significant enrichment of Candida, Mortierella and Boothiomyces. The redundancy analysis showed that plant physiological characteristics, soil ammonium-nitrogen content were significantly correlated with the soil microbial community. Therefore, heat stress altered the soil microbial community structure, and affected the availability of soil available nitrogen, which in turn affected the physiological characteristics of R. simsii. We suggest that soil microbial community may play an important role in plant resistance to heat stress, and its mechanism deserves further study.