Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of chitosan/gelatin hydrogels incorporation of biphasic calcium phosphate nanoparticles for bone tissue engineering

Abstract The chitosan/gelatin hydrogel incorporated with biphasic calcium phosphate nanoparticles (BCP-NPs) as scaffold (CGB) for bone tissue engineering was reported in this article. Such nanocomposite hydrogels were fabricated by using cycled freeze-thawing method, of which physicochemical and biological properties were regulated by adjusting the weight ratio of chitosan/gelatin/BCP-NPs. The needle-like BCP-NPs were dispersed into composites uniformly, and physically cross-linked with chitosan and gelatin, which were identified via Scanning Electron Microscope (SEM) images and Fourier Transform Infrared Spectroscopy (FT-IR) analysis. The porosity, equilibrium swelling ratio, and compressive strength of CGB scaffolds were mainly influenced by the BCP-NPs concentration. In vitro degradation analysis in simulated body fluids (SBF) displayed that CGB scaffolds were degraded up to at least 30 wt% in one month. Also, CCK-8 analysis confirmed that the prepared scaffolds had a good cytocompatibility through in culturing with bone marrow mesenchymal stem cells (BMSCs). Finally, In vivo animal experiments revealed that new bone tissue was observed inside the scaffolds, and gradually increased with increasing months, when implanted CGB scaffolds into large necrotic lesions of rabbit femoral head. The above results suggested that prepared CGB nanocomposites had the potential to be applied in bone tissue engineering. Graphical Abstract
The dietary combination of essential oils and organic acids reduces Salmonella enteritidis in challenged chicks

This study was conducted to determine the effects of essential oils and organic acids (EOA) on Salmonella Enteritidis (S. Enteritidis) challenged chickens. One-day-old specific pathogen-free (SPF) chicks (250) were randomly assigned to 5 groups, with 50 birds in each group. The treatment groups were as follows: 1) basal diet, negative control group (NC); 2) basal diet + S. Enteritidis, positive control group (PC); 3) PC + 4,000 g/t of enrofloxacin (5%), antibiotic group (ENR); 4) PC + 800 g/t of EOA1, thymol-benzoic acid group (TBA); and 5) PC + 800 g/t of EOA2, cinnamylaldehyde-caproic acid group (CCA). At 7 D of age, each bird, except those in NC, was orally gavaged with 0.4 mL of a suspension of 4.4 × 109 cfu S. Enteritidis/mL. Results revealed that ENR reduced bacterial counts in the liver and spleen on days 3, 5, and 7 post-challenge more (P < 0.05) than any other treatments. However, bacterial counts in cecal contents among ENR, TBA, and CCA were similar at 5 and 7 D post-challenge but lower than those of PC. Additionally, the bacterial counts in liver, spleen, and cecum contents in TBA were lower (P < 0.05) than in PC at 3, 5, and 7 D post-challenge; the bacterial counts in spleen contents in TBA were lower (P < 0.05) than in CCA at 7 D post-challenge. Tumor necrosis factor-α contents in TBA and CCA were lower (P < 0.05) than those in PC. Also, the ratio of villus height to crypt depth in the ileum of CCA was higher (P < 0.05) than that of PC and ENR; however, there was no difference in the secretory IgA content of the jejunum among the groups. In conclusion, EOA had a bacteriostatic effect on S. Enteritidis, and the effect of the thymol-benzoic acid complex surpassed that of the cinnamaldehyde-caproic acid complex. Therefore, EOA may act as an effective antibiotic substitute for animals in the prevention and treatment of Salmonella.
Melodamide A from Melodorum fruticosum — Quantification using HPLC and one‐step‐isolation by centrifugal partition chromatography

Abstract Melodamide A, a phenolic amide from the leaves of Melodorum fruticosum Lour. , has previously shown pronounced anti‐inflammatory activity. In order to rapidly isolate larger quantities for biological testing, a fast, one‐step isolation method by centrifugal partition chromatography was developed within this study. Fractionation of the dichloromethane extract was performed with a two‐phase solvent system consisting of n‐hexane, ethyl acetate, methanol, and water (3:7:5:5, v/v), leading to the isolation of melodamide A with a purity of >90% and a yield of 6.7 w% within 32 min. The developed method can also be used in dual mode for the enrichment of further constituents like flavonoids or chalcones. In order to support the centrifugal partition chromatography method development, additionally, a high‐performance liquid chromatography method was established and validated to determine quantities of melodamide A in plant material and crude extracts. Analysis of M. fruticosum leaves and a dichloromethane extract obtained from this plant material showed a total melodamide A content of 0.19 ± 0.008 and 8.9 ± 0.249 w%, respectively.
Event-Based Adaptive Neural Tracking Control for Discrete-Time Stochastic Nonlinear Systems: A Triggering Threshold Compensation Strategy

This paper investigates the event-triggered (ET) tracking control problem for a class of discrete-time strict-feedback nonlinear systems subject to both stochastic noises and limited controller-to-actuator communication capacities. The ET mechanism with fixed triggering threshold is designed to decide whether the current control signal should be transmitted to the actuator. A systematic framework is developed to construct a novel adaptive neural controller by directly applying the backstepping procedure to the underlying system. The proposed framework overcomes the noncausality problem, avoids the possible controller-related singularity problem, and gets rid of the neural approximation of the virtual control laws. Under the ET mechanism, the corresponding ET-based actuator is put forward by introducing an ET threshold compensation operator. Such a compensation operator (with an adjustable design parameter) is subtly designed based on a hyperbolic tangent function and a sign function. The threshold compensation error is analytically characterized in terms of a time-varying parameter, and the error bound is shown to be relatively small that is dependent on the adjustable design parameter. Compared with the traditional ET-based actuator without the compensation operator, the proposed ET-based actuator exhibits several distinguished features including: 1) improvement of the tracking accuracy (especially at the triggering instants); 2) further mitigation of the communication load; and 3) enlargement of the allowable range of the ET threshold. These features are illustrated by numerical and practical examples.
Biomarker Identification Through Integrating fMRI and Epigenetics

Objective: Integration of multiple datasets is a hot topic in many fields. When studying complex mental disorders, great effort has been dedicated to fusing genetic and brain imaging data. However, an increasing number of studies have pointed out the importance of epigenetic factors in the cause of psychiatric diseases. In this study, we endeavor to fill the gap by combining epigenetics (e.g., DNA methylation) with imaging data (e.g., fMRI) to identify biomarkers for schizophrenia (SZ). Methods: We propose to combine linear regression with canonical correlation analysis (CCA) in a relaxed yet coupled manner to extract discriminative features for SZ that are co-expressed in the fMRI and DNA methylation data. Result: After validation through simulations, we applied our method to real imaging epigenetics data of 184 subjects from the Mental Illness and Neuroscience Discovery Clinical Imaging Consortium. After significance test, we identified 14 brain regions and 44 cytosine-phosphate-guanine(CpG) sites. Average classification accuracy is $\text{88.89}\%$. By linking the CpG sites to genes, we identified pathways Guanosine ribonucleotides de novo biosynthesis and Guanosine nucleotides de novo biosynthesis, and a GO term Perikaryon. Conclusion: This imaging epigenetics study has identified both brain regions and genes that are associated with neuron development and memory processing. These biomarkers contribute to a good understanding of the mechanism underlying SZ but are overlooked by previous imaging genetics studies. Significance: Our study sheds light on the understanding and diagnosis of SZ with a imaging epigenetics approach, which is demonstrated to be effective in extracting novel biomarkers associated with SZ.
Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset

ABSTRACT Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Our aim was, for a broiler dataset with a limited number of sires having both purebred and crossbred offspring generated using natural mating, to rapidly derive parentage, assess the distribution of the sire contribution to the offspring generation, and to assess breed-of-origin of alleles in crossbreds. The dataset contained genotypes for 56,075 SNPs for 5,882 purebred and 10,943 3-way crossbred offspring generated by natural mating of 164 purebred sires to 1,016 purebred and 1,386 F1 crossbred hens. Using our algorithm FindParents, joint parentage derivation for the offspring and parent generations required only 1 m 29 s to retrieve parentage for 20,253 animals considering 4,504 possible parents. FindParents was similarly accurate as a maximum likelihood based method, apart from situations where settings of FindParents did not match the genotyping error rate in the data. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 270 crossbreds and 1 to 154 purebreds. Derivation of breed-of-origin of alleles relied on phasing all genotypes, including 8,205, 372, and 720 animals from the 3 pure lines involved, and allocating haplotypes in the crossbreds to purebred lines based on observed frequencies in the purebred lines. Breed-of-origin could be derived for 96.94% of the alleles of the 1,386 F1 crossbred hens and for 91.88% of the alleles of the 10,943 3-way crossbred offspring, of which 49.49% to the sire line. The achieved percentage of assignment to the sire line was sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known. Although required number of animals may be population dependent, to increase the total percentage of assigned alleles, it seems advisable to use at least approx. 1,000 genotyped purebred animals for each of the lines involved.
Effects of allochthonous DOM input on microbial composition and nitrogen cycling genes at two contrasting estuarine sites.

Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N cycling genes (metagenomics), and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but effects on overall community composition and the representation of N cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N related functions, and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.
The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae.

The yeast family Pichiaceae, also known as the 'methylotrophs clade', is a relatively little-studied group of yeasts despite its economic and clinical relevance. To explore genome evolution and synteny relationships within this family, we developed a Methylotroph Gene Order Browser (MGOB, http://mgob.ucd.ie) similar to our previous gene order browsers for other yeast families. The dataset contains genome sequences from nine Pichiaceae species, including our recent reference sequence of Pichia kudriavzevii. As an example, we demonstrate conservation of synteny around the MOX1 locus among species both containing and lacking the MOX1 gene for methanol assimilation. We found ancient clusters of genes that are conserved as adjacent between Pichiaceae and Saccharomycetaceae. Surprisingly, we found evidence that the locations of some centromeres have been conserved among Pichiaceae species, and between Pichiaceae and Saccharomycetaceae, even though the centromeres fall into different structural categories-point centromeres, inverted repeats, and retrotransposon cluster centromeres.
Possibilistic Fuzzy C-means Topic Modelling for Twitter Sentiment Analysis

: Social media are generating an enormous amount of sentiment data in the form of companies getting their customers’ opinions on their products, political sentiment analysis and movie reviews, etc. In this scenario, twitter sentiment analysis is undertaken for classifying and identifying sentiments or opinions expressed by people in their tweets. Usually, the raw tweets consist of more noises in terms of URLs, stop-words, positive emojis and negative emojis, which are essentially reduced. After pre-processing, an effective topic modelling methodology Latent Dirichlet Allocation (LDA) is implemented for extracting the keywords and identifying the concerned topics. The extracted key words are utilized for twitter sentiment analysis using Possibilistic fuzzy c-means (PFCM) approach. The proposed clustering method finds the optimal clustering heads from the sentimental contents of twitter-sanders-apple2 database. The acquired results are obtained in two forms such as positive and negative. Finally, the experimental outcome shows that the proposed approach improved accuracy in twitter sentiment analysis up to 3-3.5% compared to the existing methods: pattern based approach and ensemble method.
The association of multimorbidity within cardio-metabolic disease domains with dietary patterns: A cross-sectional study in 129 369 men and women from the Lifelines cohort

Background Multimorbidity is considered a major challenge for current health care. Lifestyle interventions, as a broad and generic approach, may have the potential to improve the management of care among patients with multimorbidity. The objective of this study was to evaluate the association of multimorbidity defined within the cardiometabolic disease domains with dietary patterns, representing habitual dietary intake. Design We studied 129 369 participants from the Lifelines Cohort study (42% male, 45±13 years (range 18–93)) in which diet was assessed using a 110-item food frequency questionnaire. A composite morbidity score was applied in multivariable ordered logistic regression to test the association with dietary patterns derived by principal components analysis, based on sex-specific dietary pattern scores. Results Four dietary patterns were retained, accounting for 26.6% of the variation in overall diet. After control for potential confounders, men and women in the highest quintile of “meat, alcohol and potato pattern” and “snack pattern” had a higher likelihood of having higher morbidity scores than those in the lowest quintile (e.g. men: OR = 1.83(95% CI:1.71–1.97), OR = 1.18(95% CI 1.11–1.27 respectively). The opposite was observed with respect to the “bread and sweets pattern” and “vegetable, fish and fruit pattern” (e.g. women: OR = 0.88(95% CI: 0.81–0.96), OR = 0.86(95% CI 0.81–0.92 respectively). The association partially attenuated after adjusting for BMI, but the associations remained significant among men. Conclusions Robust associations between dietary patterns and multimorbidity within the cardiometabolic domain, in particular a “meat, alcohol and potato pattern”, suggest an important opportunity of dietary interventions in multimobidity prevention. Generic prevention strategies based on population derived dietary patterns may have the potential to enhance lifestyle management among people with multimorbidity.
Biomechanical Role and Motion Contribution of Ligaments and Bony Constraints in the Elbow Stability: A Preliminary Study

In flexion–extension motion, the interaction of several ligaments and bones characterizes the elbow joint stability. The aim of this preliminary study was to quantify the relative motion of the ulna with respect to the humerus in two human upper limbs specimens and to investigate the constraints role for maintaining the elbow joint stability in different section conditions. Two clusters of four markers were fixed respectively to the ulna and humerus, and their trajectory was recorded by a motion capture system during functional orthopedic maneuver. Considering the posterior bundle of medial collateral complex (pMUCL) and the coronoid, two section sequences were executed. The orthopedic maneuver of compression, pronation and varus force was repeated at 30°, 60° and 90° flexion for the functional investigation of constraints. Ulna deflection was compared to a baseline elbow flexion condition. With respect to the intact elbow, the coronoid osteotomy influences the elbow stability at 90° (deflection = 11.49 ± 17.39 mm), while small differences occur at 30° and 60°, due to ligaments constraint. The contemporary pMUCL section and coronoid osteotomy causes elbow instability, with large deflection at 30° (deflection = 34.40 ± 9.10 mm), 60° (deflection = 45.41 ± 18.47 mm) and 90° (deflection = 52.16 ± 21.92 mm). Surgeons may consider the pMUCL reconstruction in case of unfixable coronoid fracture.
Egg Yolk Antioxidants Profiles: Effect of Diet Supplementation with Linseeds and Tomato-Red Pepper Mixture before and after Storage

This study evaluated the effect of dietary incorporation of linseed alone or along with dried tomato paste-pepper powder mix on egg physical characteristics, antioxidant profiles, lipid oxidative status, and yolk coloration before and after storage at 4 °C for one month. Sixty Novogen White laying hens, 27 weeks-old, were divided into three groups and given 100 g/hen/day of a standard diet (C), standard diet containing 4.5% of ground linseed (L), linseed diet containing 1% of dried tomato paste and 1% of sweet red pepper (LTP). Linseeds increased (p < 0.05) egg yolk antioxidant capacity but not lipid oxidative stability (p > 0.05). However, dietary inclusion of LTP did not improve fresh egg yolk antioxidant activity and lipid oxidation stability (p > 0.05). With reference to the stored eggs, only antioxidant activity measured by phosphomolybdenum reduction and lipid oxidative stability were influenced (p < 0.05) by the dietary treatment. Fresh egg yolk of hens fed on linseeds tended to have a slightly more yellow, redder, and less light color than the eggs of hens fed with the control diet. Dietary supplementation of LTP increased (p < 0.05) the Roche yolk color fan (RYCF) score and redness (a*) and decreased (p < 0.05) lightness (L*) without affecting (p > 0.05) saturation (C*). Storage of hens’ eggs fed on the control diet did not influence (p > 0.05) yolk color.
Assembly of B4GALT1/ST6GAL1 heteromers in the Golgi membranes involves lateral interactions via highly charged surface domains

β-1,4-Galactosyltransferase 1 (B4GALT1) and ST6 β-galactoside α-2,6-sialyltransferase 1 (ST6GAL1) catalyze the successive addition of terminal β-1,4–linked galactose and α-2,6–linked sialic acid to N-glycans. Their exclusive interaction in the Golgi compartment is a prerequisite for their full catalytic activity, whereas a lack of this interaction is associated with cancers and hypoxia. To date, no structural information exists that shows how glycosyltransferases functionally assemble with each other. Using molecular docking simulations to predict interaction surfaces, along with mutagenesis screens and high-throughput FRET analyses in live cells to validate these predictions, we show here that B4GALT1 and ST6GAL1 interact via highly charged noncatalytic surfaces, leaving the active sites exposed and accessible for donor and acceptor substrate binding. Moreover, we found that the assembly of ST6GAL1 homomers in the endoplasmic reticulum before ST6GAL1 activation in the Golgi utilizes the same noncatalytic surface, whereas B4GALT1 uses its active-site surface for assembly, which silences its catalytic activity. Last, we show that the homomeric and heteromeric B4GALT1/ST6GAL1 complexes can assemble laterally in the Golgi membranes without forming cross-cisternal contacts between enzyme molecules residing in the opposite membranes of each Golgi cisterna. Our results provide detailed mechanistic insights into the regulation of glycosyltransferase interactions, the transitions between B4GALT1 and ST6GAL1 homo- and heteromers in the Golgi, and cooperative B4GALT1/ST6GAL1 function in N-glycan synthesis.
Neuroimaging in Pediatric Epilepsy

Pediatric epilepsy presents with various diagnostic challenges. Recent advances in neuroimaging play an important role in the diagnosis, management and in guiding the treatment of pediatric epilepsy. Structural neuroimaging techniques such as CT and MRI can identify underlying structural abnormalities associated with epileptic focus. Functional neuroimaging provides further information and may show abnormalities even in cases where MRI was normal, thus further helping in the localization of the epileptogenic foci and guiding the possible surgical management of intractable/refractory epilepsy when indicated. A multi-modal imaging approach helps in the diagnosis of refractory epilepsy. In this review, we will discuss various imaging techniques, as well as aspects of structural and functional neuroimaging and their application in the management of pediatric epilepsy.
Data-Driven Digital Advertising with Uncertain Demand Model in Metro Networks

Nowadays most metro advertising systems schedule advertising slots on digital advertising screens to achieve the maximum exposure to passengers by exploring passenger demand models. However, our empirical results show that these passenger demand models experience uncertainty at fine temporal granularity (e.g., per min). As a result, for fine-grained advertisements (shorter than one minute), a scheduling based on these demand models cannot achieve the maximum advertisement exposure. To address this issue, we propose an online advertising approach, called FineUDM, based on the uncertain passenger demand modeling for both entering passengers and exiting passengers. FineUDM combines coarse-grained statistical demand modeling and fine-grained real-time demand modeling by leveraging historical passenger demands, real-time card-swiping records, and passenger mobility patterns. Based on this uncertain demand model, it schedules advertising time online based on robust receding horizon control to maximize the advertisement exposure. We evaluate the proposed approach based on an one-month sample from our 530 GB real-world metro fare dataset with 16 million cards. The results show that our approach provides a 61.5 percent lower traffic prediction error and 20 percent improvement on advertising efficiency on average.