Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium Vibrio fluvialis A8 Through Horizontal Gene Transfer

Agarose-oligosaccharide production from agar degradation by agarase exhibits lots of advantages and good application prospects. In this study, a novel agar-degrading bacterium Vibrio sp. A8 was isolated from a red algae in the South China Sea. The whole genome sequencing with comparative genomic and secretomic analysis were used to better understand its genetic components about agar degradation. This strain exhibited good agarase production in artificial seawater after culture optimization. The complete genome (4.88 Mb) of this strain comprised two circular chromosomes (3.19 and 1.69 Mb) containing 4,572 protein-coding genes, 108 tRNA genes and 31 rRNA genes. This strain was identified as Vibrio fluvialis A8 by comparative genomic analysis based on genome phylogenetic tree and average nucleotide identity (ANI) similarity. Different from other 20 similar strains including three strains of the same species, V. fluvialis A8 possessed unique agar degradation ability with four β-agarases (GH50) and one α-1,3-L-NA2 hydrolase (GH117) due to the horizontal gene transfer. Secretomic analysis showed that only β-agarase (gene 3152) was abundantly expressed in the secretome of V. fluvialis A8. This agarase had a good substrate specificity and wide work conditions in complex environments, suggesting its potential application for agarose-oligosaccharide production.
MNX1 Promotes Malignant Progression of Cervical Cancer via Repressing the Transcription of p21cip1

Motor neuron and pancreas homeobox 1 (MNX1) is a development-related genes and has been found to be highly expressed in several cancers. However, its biological function in cervical cancer remains largely unexplored. QRT-PCR, western blot, and IHC showed that MNX1 was abnormally overexpressed in cervical cancer tissues and cell lines. The high expression level of MNX1 correlated with poorer clinicopathologic characteristics in cervical cancer patients. Evaluated by RTCA (Real Time Cellular Analysis) proliferation assay, colony formation assay, EdU assay, transwell assay, and matrigel assay, we found that knockdown of MNX1 inhibited proliferation, migration and invasion of cervical cancer in vitro, while overexpression of MNX1 promoted malignant phenotype of cervical cancer. And subcutaneous xenograft model confirmed the malignant phenotype of MNX1 in vivo. Furthermore, flow cytometry, chromatin immunoprecipitation, and luciferase reporter assay indicated that MNX1 accelerated cell cycle transition by transcriptionally downregulating cyclin-dependent kinases p21cip1. In summary, our study revealed that MNX1 exerted an oncogenic role in cervical cancer via repressing the transcription of p21cip1 and thus accelerating cell cycle progression. Our results suggested that MNX1 was a potential diagnostic marker and therapeutic target for cervical cancer patients.
Plasma microRNA Array Analysis Identifies Overexpressed miR-19b-3p as a Biomarker of Bipolar Depression Distinguishing From Unipolar Depression

Objectives The clinical characteristics of bipolar disorder (current major depressive episode) (BD) overlap with unipolar depressive disorder (UD), which makes it difficult to perform an accurate diagnosis. We identified plasma microRNAs (miRNAs) that distinguished BD from UD and explored the relationship between miRNA expression levels and clinical characteristics. Methods Total miRNAs from blood plasma from seven UD patients, seven BD patients, and six controls were analyzed. The identified miRNAs were validated in a separate population group. Depression severity and early life adversities were assessed. Bioinformatic analysis was conducted to investigate the target genes that were identified and the pathways associated with the altered miRNAs. Results Compared to controls, 42 miRNAs were differentially expressed in patients. miR-19b-3p, miR-3921, and miR-1180-3p were selected to validate the microarray results. Only miR-19b-3p was validated as down-regulated in patients. The primary predicted genes associated with miR-19b-3p were MAPK1, PTEN, and PRKAA1. The most relevant KEGG pathways included mTOR, FoxO, and the PI3-K/Akt signaling pathway. BD patients were more likely to have higher expression levels of miR-19b-3p and more severe childhood trauma experience compared to UD patients. Conclusions Plasma miR-19b-3p is a potential non-invasive biomarker that might be useful in distinguishing UD from BD. miR-19b3p was predicted to be involved in the pathway of inflammatory dysregulation associated with experiencing early childhood trauma.
Atypical Frequency Sweep Processing in Chinese Children With Reading Difficulties: Evidence From Magnetoencephalography

Chinese lexical tones determine word meaning and are crucial in reading development. Reduced tone awareness is widely reported in children with reading difficulties (RD). Lexical-tone processing requires sensitivity to frequency-modulated sound changes. The present study investigates whether reduced tone awareness in children with RD is reflected in basic auditory processing and the level at which the breakdown occurs. Magnetoencephalographic techniques and an oddball paradigm were used to elicit auditory-related neural responses. Five frequency sweep conditions were established to mirror the frequency fluctuation in Chinese lexical tones, including one standard (level) sweep and four deviant sweeps (fast-up, fast-down, slow-up, and slow-down). A total of 14 Chinese-speaking children aged 9–12 years with RD and 13 age-matched typically developing children were recruited. The participants completed a magnetoencephalographic data acquisition session, during which they watched a silent cartoon and the auditory stimuli were presented in a pseudorandomized order. The results revealed that the significant between-group difference was caused by differences in the level of auditory sensory processing, reflected by the P1m component elicited by the slow-up frequency sweep. This finding indicated that auditory sensory processing was affected by both the duration and the direction of a frequency sweep. Sensitivity to changes in duration and frequency is crucial for the processing of suprasegmental features. Therefore, this sensory deficit might be associated with difficulties discriminating two tones with an upward frequency contour in Chinese.
Radiomic-Based Quantitative CT Analysis of Pure Ground-Glass Nodules to Predict the Invasiveness of Lung Adenocarcinoma

Objectives: To investigate the performance of radiomic-based quantitative analysis on CT images in predicting invasiveness of lung adenocarcinoma manifesting as pure ground-glass nodules (pGGNs). Methods: A total of 275 lung adenocarcinoma cases, with 322 pGGNs resected surgically and confirmed pathologically, from January 2015 to October 2017 were enrolled in this retrospective study. All nodules were split into training and test cohorts randomly with a ratio of 4:1 to establish models to predict between pGGN-like adenocarcinoma in situ (AIS)/minimally invasive adenocarcinoma (MIA) and invasive adenocarcinoma (IVA). Radiomic feature extraction was performed using Pyradiomics with semi-automatically segmented tumor regions on CT scans that were contoured with an in-house plugin for 3D-Slicer. Random forest (RF) and support vector machine (SVM) were used for feature selection and predictive model building in the training cohort. Three different predictive models containing conventional, radiomic, and combined models were built on the basis of the selected clinical, radiological, and radiomic features. The predictive performance of each model was evaluated through the receiver operating characteristic curve (ROC) and the area under the curve (AUC). The predictive performance of two radiologists (A and B) and our radiomic predictive model were further investigated in the test cohort to see if radiomic predictive model could improve radiologists' performance in prediction between pGGN-like AIS/MIA and IVA. Results: Among 322 nodules, 48 (14.9%) were AIS and 102 (31.7%) were MIA with 172 (53.4%) for IVA. Age, diameter, density, and nine meaningful radiomic features were selected for model building in the training cohort. Three predictive models showed good performance in prediction between pGGN-like AIS/MIA and IVA (AUC > 0.8, P < 0.05) in both training and test cohorts. The AUC values in the test cohort were 0.824 (95% CI, 0.723–0.924), 0.833 (95% CI, 0.733–0.934), and 0.848 (95% CI, 0.750–0.946) for conventional, radiomic, and combined models, respectively. The predictive accuracy was 73.44 and 59.38% for radiologist A and radiologist B in the test cohort and was improved dramatically to 79.69 and 75.00% with the aid of our radiomic predictive model. Conclusion: The predictive models built in our study showed good predictive power with good accuracy and sensitivity, which provided a non-invasive, convenient, economic, and repeatable way for the prediction between IVA and AIS/MIA representing as pGGNs. The radiomic predictive model outperformed two radiologists in predicting pGGN-like AIS/MIA and IVA, and could significantly improve the predictive performance of the two radiologists, especially radiologist B with less experience in medical imaging diagnosis. The selected radiomic features in our research did not provide more useful information to improve the combined predictive model's performance.
Coactivation pattern analysis reveals altered salience network dynamics in children with autism spectrum disorder

Brain connectivity studies of autism spectrum disorder (ASD) have historically relied on static measures of functional connectivity. Recent work has focused on identifying transient configurations of brain activity, yet several open questions remain regarding the nature of specific brain network dynamics in ASD. We used a dynamic coactivation pattern (CAP) approach to investigate the salience/midcingulo-insular (M-CIN) network, a locus of dysfunction in ASD, in a large multisite resting-state fMRI dataset collected from 172 children (ages 6–13 years; n = 75 ASD; n = 138 male). Following brain parcellation by using independent component analysis, dynamic CAP analyses were conducted and k-means clustering was used to determine transient activation patterns of the M-CIN. The frequency of occurrence of different dynamic CAP brain states was then compared between children with ASD and typically developing (TD) children. Dynamic brain configurations characterized by coactivation of the M-CIN with central executive/lateral fronto-parietal and default mode/medial fronto-parietal networks appeared less frequently in children with ASD compared with TD children. This study highlights the utility of time-varying approaches for studying altered M-CIN function in prevalent neurodevelopmental disorders. We speculate that altered M-CIN dynamics in ASD may underlie the inflexible behaviors commonly observed in children with the disorder.
Production of Silver Nanoparticles by Marigold Extract

Silver nanoparticles are widely used in manufacturing of different products considering their unique physical and chemical properties. Also they have been noticed in medical diagnosis and treatment because of their antibacterial properties. Physical and chemical methods of producing nanoparticles, are expensive and are not safe enough as toxic substances may remain in the final preparations. To solve this problem, biological production of nanoparticles is considered as an efficient alternative method. In present study, synthesis of silver nanoparticles via seeds, petals, roots, and hairy root extracts of Calendula officinalis were performed. These nanoparticles were characterized by means of spectrophotometer, particle size analyzer and transmission electron microscope. Nanoparticles which were synthesized by hairy root extract showed the highest absorption at 430 nm (1/6 a.u) and the smallest size (5/3 nm), in comparison to other examined particles. Results confirmed the better performance of hairy root extracts in the synthesis of silver nanoparticles.
Learning Off-Policy with Online Planning

We propose Learning Off-Policy with Online Planning (LOOP), combining the techniques from model-based and model-free reinforcement learning algorithms. The agent learns a model of the environment, and then uses trajectory optimization with the learned model to select actions. To sidestep the myopic effect of fixed horizon trajectory optimization, a value function is attached to the end of the planning horizon. This value function is learned through off-policy reinforcement learning, using trajectory optimization as its behavior policy. Furthermore, we introduce "actor-guided" trajectory optimization to mitigate the actor-divergence issue in the proposed method. We benchmark our methods on continuous control tasks and demonstrate that it offers a significant improvement over the underlying model-based and model-free algorithms.
Abondance relative des tabanidés dans la région des savanes de Côte d'Ivoire

Tabanids were caught with Nzi traps to study their presence, abundance, seasonal variation, ecological preferences and species diversity. The study was conducted over four seasons in four habitats (savanna, forest, gallery, and corral) in four townships in the main two livestock departments of North and Northwest Ivory Coast (Odienne and Korhogo). Out of 3104 caught specimens, 4 genera and 16 tabanid species were identified. The most abundant of caught species were Tabanus taeniola Palisot de Beauvois, 1807 (26.4%), T. par Walker, 1854 (15.6%), T. laverani Surcouf, 1907 (14.9%), and Chrysops distinctipennis Austen, 1906 (12.3%). The least abundant species were Atylotus albipalpus Walker, 1850 (6.9%), Chrysops longicornis Macquart, 1838 (6.9%), T. brumpti Surcouf, 1907 (4.8%), T. gratus Loew, 1858 (3.7%), At. agrestis Wiedemann, 1828 (2.5%), At. fuscipes Ricardo, 1908 (1.8%), Ancala necopina Austen, 1912 (1.5%), T. biguttatus Wiedemann, 1830 (1.4%), T. ricardea Surcouf, 1906 (0.5%), T. boueti Surcouf, 1907 (0.4%), T. pluto Walker, 1854 (0.3%), and An. fasciata Fabricius, 1775 (0.2%). The largest numbers of tabanids were caught in the gallery, and the fewest in the forest. There were more catches in the Odienne department than in that of Korhogo. An abundance peak occurred in March during the hot dry season, except for Korondougou township, where a peak occurred in June during the rainy season. In addition, 2471 Stomoxyinae were captured: Stomoxys niger Macquart, 1851 (70.7%) and S. calcitrans Linnaeus, 1758 (29.3%). The Stomoxyinae, represented by two species only, made up about 45% of the biting flies captured. They will have to be reckoned with when evaluating the impact of biting insects on cattle.
Comparison of gingival crevicular fluid and serum Human Beta Defensin-2 levels between periodontal health and disease.

BACKGROUND The aim of this study was to evaluate the serum and gingival crevicular fluid (GCF) human beta defensin-2 (hBD-2) levels, an antimicrobial peptide that takes roles in inflammatory diseases, in patients with chronic periodontitis (CP). SUBJECTS AND METHODS A total of one hundred one individuals, 59 controls, and 42 patients with CP, participated in this study. Clinical index measurements were recorded during the periodontal examination, and radiographic evaluation was also performed. The serum and gingival crevicular fluid (GCF) samples were taken from all of the participants, and the hBD-2 levels were determined biochemically by Enzyme-Linked Immuno-Sorbent Assay (ELISA). RESULTS In our study, hBD-2 GCF levels in CP (stagesII-IV periodontitis based onthe new 2018 classification of periodontal diseases)group (2.77 ng/30sec) were higher than in the periodontally healthy (2.51 ng/30sec; p=0.047) individuals. In contrast, serum hBD-2 levels in CP (2.92 ng/mL) were lower compared to those of healthy controls (7.75 ng/mL, p<0.001). CONCLUSION Interestingly, our results showed that while higher hBD-2 GCF levels are associated with CP, lower serum hBD-2 levels were detected in CP.
Precision transcriptomics of viral foci reveals the spatial regulation of immune‐signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potato

SUMMARY Whereas the activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to the restriction of the pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny‐1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels in order to reveal the spatiotemporal regulation of the immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA‐deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed and the spread of the virus is not arrested at the site of infection. RBOHD is required for the spatial accumulation of SA, and conversely RBOHD is under the transcriptional regulation of SA. Using spatially resolved RNA‐seq, we also identified spatial regulation of an UDP‐glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.
Opioid and Dopamine Genes Interact to Predict Naltrexone Response in a Randomized Alcohol Use Disorder Clinical Trial.

BACKGROUND While the opiate antagonist, naltrexone, is approved for Alcohol Use Disorder (AUD), not everyone benefits. This study evaluated whether the OPRM1 SNP rs1799971 interacts with the dopamine transporter gene DAT1/SLC6A3 VNTR rs28363170 or the catechol-o-methyltransferase (COMT) gene SNP rs4680 in predicting naltrexone response. METHODS Individuals who met DSM-IV alcohol dependence were randomly assigned to naltrexone (50 mg/day) or placebo based on their OPRM1 genotype (75 G allele carriers and 77 A allele homozygotes) and also genotyped for DAT1 VNTR (9 vs 10 repeats) or COMT SNP (val/val vs. met carriers). Heavy drinking days (%HDD) were evaluated over 16 weeks and at the end of treatment. Effect sizes (d) for naltrexone response were calculated based on genotypes. RESULTS Naltrexone, relative to placebo, significantly reduced %HDD among OPRM1 G carriers who also had DAT1 10/10 (p=0.021, d=0.72) or COMT val/val genotypes (p=0.05, d=0.80), and to a lesser degree in those OPRM1 A homozygotes who were also DAT1 9-repeat carriers (p=0.09, d=0.70) or COMT met carriers (p=0.03, d=0.63). All other genotype combinations showed no differential response to naltrexone. Diarrhea/abdominal pain was more prominent in OPRM1 A homozygotes who were also DAT 9 or COMT met carriers. CONCLUSIONS These results suggest that Individuals with AUD with a more opioid-responsive genotype (OPRM1 G carriers) respond better to naltrexone if they have genotypes indicating normal/less dopamine tone (DAT1 10,10 or COMT val,val), while those with a less responsive opioid-responsive genotype (OPRM1 A homozygotes) respond better to naltrexone if they have genotypes indicating greater dopamine tone (DAT1 9-repeat or COMT met carriers). These results could lead to more personalized AUD treatments.
Effects of maternal high‐fat/high sucrose diet on hepatic lipid metabolism in rat offspring

Maternal obesity and/or high‐fat diet during pregnancy predispose the offspring to metabolic disease. It is however unclear how pre‐natal and post‐natal exposure respectively affect the risk of hepatic steatosis and the trajectory towards non‐alcoholic steatohepatitis in the offspring. We investigate hepatic lipid metabolism and how these factors are related to metabolic outcome in new born and young rats. Rat dams were exposed to a high‐fat/high sucrose (HFHS) diet for 17 weeks prior to mating and during pregnancy. After birth, female offspring were killed and male offspring were cross‐fostered, creating four groups; Control‐born pups lactated by control (CC) or HFHS dams (CH) and HFHS‐born pups lactated by control (HC) or HFHS dams (HH). At 4 weeks of age, pups were killed and metabolic markers in plasma were assayed, together with hepatic lipid composition and expression of relevant genes. Female HFHS neonates had smaller livers at birth (P < .05), a reduced hepatic lipid content (P < .05) and altered lipid composition. The post‐natal environment dominated the metabolic profile in the male offspring at 4 weeks of age. Offspring exposed to a HFHS environment post‐natally had increased adiposity (P < .0001), increased hepatic triacylglycrol accumulation (P < .0001), and an altered lipid profile with elevated n‐6 polyunsaturated fatty acid (PUFA) levels (P < .0001) and a reduction in ceramide (P < .001) and monounsaturated fatty acid (MUFA) (P < .0001). In summary, maternal HFHS diet during gestation affects the hepatic lipid profile in neonates. The pre‐natal exposure becomes less pronounced in young male offspring at 4 weeks of age, where the post‐natal diet has the largest impact.
Bridging Worlds in Reinforcement Learning with Model-Advantage

Despite the breakthroughs achieved by Reinforcement Learning (RL) in recent years, RL agents often fail to perform well in unseen environments. This inability to generalize to new environments prevents their deployment in the real world. To help measure this gap in performance, we introduce model-advantage - a quantity similar to the well-known (policy) advantage function. First, we show relationships between the proposed model-advantage and generalization in RL — using which we provide guarantees on the gap in performance of an agent in new environments. Further, we conduct toy experiments to show that even a sub-optimal policy (learnt with minimal interactions with the target environment) can help predict if a training environment (say, a simulator) helps learn policies that generalize. We then show connections with Model Based RL.
A Microfoundation of Centrifugal Dynamics in Party Systems

When explaining the polarization of party systems, Satori’s (1976) typology represents one of the central concepts. Here the direction of party competition is affected by an occupied political center and a bilateral opposition. The macro-level explanans and explanandum are based on the behavior of parties and voters. A party system will only polarize if the voting behavior and/or the party positions change. Thus, the following research question arises: Which influences on actors in party competition determine the correlation on the macro-level? In the first step the link between coalition formation and the behavior of parties and voters is discussed. In the logic of Sartori the accountability of coalition parties, the cooperation of parties and the possible dissatisfaction of voters with governing parties are plausible factors. Secondly, these causal mechanisms are tested in an agent-based model. A Microfoundation of Centrifugal Dynamics in Party Systems Johannes Schmitt