Miracle-dz/UniFAR-FTUs huggingface dataset:
The Use of the Neoglycolipid-Based Oligosaccharide Microarray System in the Diagnosis of Endometriosis – Preliminary Study

Objective Endometriosis presents diagnostic challenges, and there is a need for developing novel biomarkers with satisfactory specificity and sensitivity. Glycomics, exploring glycosylation changes in glycoproteins, offers potential solutions. The aim of this study was to analyze the carbohydrate-binding properties of IgG and IgM antibodies in the plasma and peritoneal fluid samples and to identify any differences in the presence and the specificities of anti-carbohydrate antibodies in the endometriosis patient and the controls. Methods Multicenter study was conducted in Poland between 2018 and 2019. Plasma and peritoneal fluid samples were collected from women undergoing laparoscopic surgery. Endometriosis patients (n=8) and controls (n=8), matched for cycle phase and disease stage, were selected. The neoglycolipid-based oligosaccharide microarray system was used to investigate IgG and IgM antibody binding properties to glycan-related probes in biological materials. Results In peritoneal fluid samples, IgM binding to the following probes was significantly higher in endometriosis: GSC-915-4 (new), LNFP-I, NeuAcα-(6’)LNnO (F1), B-like decaosylceramide, log10(GM1-penta), and log10(GSC-915-5). In a control group higher IgG binding to log10(Orsay-5-AO) was observed. In plasma samples, endometriosis showed higher IgG binding to log10(NeuAcα-(6’)LNnO (F1)) and lower IgG binding to Gal2GlcNAc(1-3)-AO. After Benjamin–Hochberg correction, differences were not significant. Effect sizes highlighted some glycan probes in both plasma and peritoneal fluid. Strong correlations were observed among binding to certain glycan probes. Conclusion This preliminary study suggests glycomics’ potential contribution to endometriosis diagnosis and understanding of its pathophysiology. Neoglycolipid-based microarrays hold promise for non-invasive endometriosis diagnostic tools. Further investigations with larger cohorts are warranted to validate these findings and explore potential correlations with antibody levels in plasma and peritoneal fluid. Glycomics emerges as a valuable diagnostic asset in endometriosis research.
SoUth Korean study to PrEvent cognitive impaiRment and protect BRAIN health through Multidomain interventions via facE-to-facE and video communication plaTforms in mild cognitive impairment (SUPERBRAIN-MEET): Protocol for a Multicenter Randomized Controlled Trial

Background and Purpose The SoUth Korea study to PrEvent cognitive impaiRment and protect BRAIN health through lifestyle intervention (SUPERBRAIN) proved the feasibility of multidomain intervention for elderly people. One-quarter of the Korean population over 65 years of age has mild cognitive impairment (MCI). Digital health interventions may be cost-effective and have fewer spatial constraints. We aim to examine the efficacy of a multidomain intervention through both face-to-face interactions and video communication platforms using a tablet personal computer (PC) application in MCI. Methods Three hundred participants aged 60–85 years, with MCI and at least one modifiable dementia risk factor, will be recruited from 17 centers and randomly assigned in a 1:1 ratio to the multidomain intervention and the waiting-list control groups. Participants will receive the 24-week intervention through the tablet PC SUPERBRAIN application, which encompasses the following five elements: managing metabolic and vascular risk factors, cognitive training, physical exercise, nutritional guidance, and boosting motivation. Participants will attend the interventions at a facility every 1–2 weeks. They will also engage in one or two self-administered cognitive training sessions utilizing the tablet PC application at home each week. They will participate in twice or thrice weekly online exercise sessions at home via the ZOOM platform. The primary outcome will be the change in the total scale index score of the Repeatable Battery for the Assessment of Neuropsychological Status from baseline to study end. Conclusions This study will inform the effectiveness of a comprehensive multidomain intervention utilizing digital technologies in MCI. Trial Registration ClinicalTrials.gov Identifier: NCT05023057
Garlic (Allium sativum) and mushroom (Agaricus bisporus) powder: Investigation of performance, immune organs and humoural and cellular immune response in broilers

Abstract Background Alternatives to antibiotics have been suggested by banning their use in the poultry industry. Garlic and mushroom are two important phytobiotic compounds in poultry nutrition. Objectives This study was conducted to evaluate the effects of supplementing diets with garlic and mushroom powder (MP) on growth performance, humoural and cellular immunity, and white blood cell counts of broiler chickens. Methods Five hundred and seventy‐six 1‐day‐old male broiler chickens (Ross 308) were assigned to 8 treatments with 6 replications (12 birds per replication) based on a completely randomized design in a factorial arrangement of 4 × 2 with 4 levels of garlic powder (GP; 0.00%, 0.50%, 1.00%, and 1.50%) and two levels of MP (0.00% and 1.00%). Results No significant effects of GP and MP on the growth performance and cutaneous basophil hypersensitivity were observed (p > 0.05). According to the regression equation, with increasing levels of GP in the diets, the relative weight of the bursa of Fabricius and thymus increased (p < 0.05). The effect of increasing levels of GP on the Newcastle disease virus (NDV) titre was greater in the absence of MP (p < 0.05). With increasing levels of GP in the diets, the percentages of lymphocytes and heterophils to lymphocytes ratio increased and reduced, respectively (p < 0.05). Conclusions This experiment has revealed that increasing the level of GP improved the immune response of broilers without affecting performance. The effect of increasing the level of GP on the NDV titre was more significant in the absence of MP.
Giving fruits and vegetables a tax break: lessons from a Dutch attempt

Objective: Food taxation can improve diets by making unhealthy foods more expensive and by making healthy foods cheaper. In the Netherlands, a political window of opportunity arose in December 2021 to reduce the value-added tax (VAT) on fruits and vegetables to zero percent. The policy is now facing institutional friction along several fronts, however, delaying and potentially averting its implementation. We analysed this institutional friction to inform future food tax policies. Design: We qualitatively analysed open-access fiscal and health experts’ position papers about benefits and downsides of the zero-rate that were discussed with members of parliament in June 2023. Setting: The Netherlands. Participants: Not applicable. Results: Health and fiscal experts expressed noticeably different viewpoints towards the utility of the zero-rate. One important argument fiscal experts based their negative advice upon pertained to the legal restrictions for distinguishing between healthier and unhealthier forms of fruits and vegetables (i.e. the principle of neutrality). A zero-rate VAT on unhealthier forms of fruits and vegetables, e.g. processed cucumber, mixed with salt and sugar, would be undesirable, but differentiating between raw and processed cucumber would offend the neutrality principle. Conclusions: The Dutch attempt to give fruits and vegetables a tax break highlights the need for crystal-clear food classifications when designing food tax policies. Public health nutritionists should combine classifications based on caloric density, palatability, degree of processing and nutrient content to provide a database for evidence-informed tax differentiation according to food item healthfulness.
Prognostic role of mesangial IgM deposition in IgA nephropathy: a long-term cohort study

Abstract Background The clinical significance of mesangial immunoglobulin (Ig) M deposition in IgA nephropathy (IgAN) has been less explored and remains a topic of debate. Therefore, our study aimed to investigate the prognostic value of mesangial IgM deposition in a long-term follow-up cohort of IgAN patients. Methods A unicentric retrospective study was conducted on 93 consecutive IgAN patients (median age 41 years, 68% male, eGFR 48.7 mL/min, proteinuria 1.1 g/g) from 2010 to 2015. They were followed until end-stage kidney disease (ESKD), death, or until the end of the study in January 2021, with a median follow-up of 7 years. An independent pathologist evaluated the IgM immunofluorescence pattern, Oxford MEST-C score, and transmission electron microscopy (TEM) lesions following a comprehensive protocol. Results In our cohort, 70% had mesangial IgM-positive deposits, while 30% were IgM-negative. Both groups were similar in age, sex, prevalence of arterial hypertension, Charlson comorbidity scores, kidney function (eGFR and proteinuria), pathology findings (Oxford MEST-C score, IgG and C3 immune deposition), and TEM analysis. Treatment with RASI and immunosuppression, and death rates were also comparable. However, 37% of IgM-positive patients progressed to ESKD, significantly higher than the 11% in the IgM-negative group. Univariate and multivariate Cox proportional hazards regression analyses identified lower eGFR, higher Oxford MEST-C score, and mesangial IgM deposits as independent factors associated with shorter kidney survival. Conclusions Our study highlights mesangial IgM deposition as a potential risk factor for ESKD in patients with advanced IgAN, laying a foundation for further research in this area.
Which elements of hospital-based clinical decision support tools for the assessment and management of children with head injury can be adapted for use by paramedics in prehospital care? A systematic mapping review and narrative synthesis

Objective Hospital-based clinical decision tools support clinician decision-making when a child presents to the emergency department with a head injury, particularly regarding CT scanning. However, there is no decision tool to support prehospital clinicians in deciding which head-injured children can safely remain at scene. This study aims to identify clinical decision tools, or constituent elements, which may be adapted for use in prehospital care. Design Systematic mapping review and narrative synthesis. Data sources Searches were conducted using MEDLINE, EMBASE, PsycINFO, CINAHL and AMED. Eligibility criteria Quantitative, qualitative, mixed-methods or systematic review research that included a clinical decision support tool for assessing and managing children with head injury. Data extraction and synthesis We systematically identified all in-hospital clinical decision support tools and extracted from these the clinical criteria used in decision-making. We complemented this with a narrative synthesis. Results Following de-duplication, 887 articles were identified. After screening titles and abstracts, 710 articles were excluded, leaving 177 full-text articles. Of these, 95 were excluded, yielding 82 studies. A further 14 studies were identified in the literature after cross-checking, totalling 96 analysed studies. 25 relevant in-hospital clinical decision tools were identified, encompassing 67 different clinical criteria, which were grouped into 18 categories. Conclusion Factors that should be considered for use in a clinical decision tool designed to support paramedics in the assessment and management of children with head injury are: signs of skull fracture; a large, boggy or non-frontal scalp haematoma neurological deficit; Glasgow Coma Score less than 15; prolonged or worsening headache; prolonged loss of consciousness; post-traumatic seizure; amnesia in older children; non-accidental injury; drug or alcohol use; and less than 1 year old. Clinical criteria that require further investigation include mechanism of injury, clotting impairment/anticoagulation, vertigo, length of time of unconsciousness and number of vomits.
Increased type-I interferon level is associated with liver damage and fibrosis in primary sclerosing cholangitis

Background: The level of type-I interferons (IFNs) in primary sclerosing cholangitis (PSC) was investigated to evaluate its association with disease activity and progression. Methods: Bioactive type-I IFNs were evaluated in a murine model of PSC and human patients’ sera using a cell-based reporter assay and ELISA techniques. In total, 57 healthy participants, 71 PSC, and 38 patients with primary biliary cholangitis were enrolled in this study. Results: Bioactive type-I IFNs were elevated in the liver and serum of multidrug resistance protein 2–deficient animals and showed a correlation with the presence of CD45+ immune cells and serum alanine transaminase levels. Concordantly, bioactive type-I IFNs were elevated in the sera of patients with PSC as compared to healthy controls (sensitivity of 84.51%, specificity of 63.16%, and AUROC value of 0.8267). Bioactive IFNs highly correlated with alkaline phosphatase (r=0.4179, p<0.001), alanine transaminase (r=0.4704, p<0.0001), and gamma-glutamyl transpeptidase activities (r=0.6629, p<0.0001) but not with serum bilirubin. In addition, patients with PSC with advanced fibrosis demonstrated significantly higher type-I IFN values. Among the type-I IFN subtypes IFNα, β and IFNω could be detected in patients with PSC with IFNω showing the highest concentration among the subtypes and being the most abundant among patients with PSC. Conclusions: The selectively elevated bioactive type-I IFNs specifically the dominating IFNω could suggest a novel inflammatory pathway that might also have a hitherto unrecognized role in the pathomechanism of PSC.
Microbial Activity in Forest Soil Under Beech, Spruce, Douglas Fir and Fir

Summary The aim of this research was to investigate the microbial activity in forest soil from different sites under deciduous and coniferous trees in Serbia. One site on Stara planina was under beech trees (Fagus sp.) while another under mixture of spruce (Picea sp.) and Douglas fir (Pseudotsuga sp.). The site on Kopaonik was under mixture of beech (Fagus sp.) and spruce (Picea sp.) trees. The site on Tara was dominantly under fir (Abies sp.), beech (Fagus sp.) and spruce (Picea sp.). The total number of bacteria, the number of actinobacteria, fungi and microorganisms involved in N and C cycles were determined using standard method of agar plates. The activities of dehydrogenase and ß-glucosidase enzymes were measured by spectrophotometric methods. The microbial activity was affected by tree species and sampling time. The highest dehydrogenase activity, total number of bacteria, number of actinobacteria, aminoheterotrophs, amylolytic and cellulolytic microorganisms were determined in soil under beech trees. The highest total number of fungi and number of pectinolytic microorganisms were determined in soil under spruce and Douglas fir trees. The correlation analyses proved the existence of statistically significant interdependency among investigated parameters.
Dual Branch Multi-Level Semantic Learning for Few-Shot Segmentation

Few-shot semantic segmentation aims to segment novel-class objects in a query image with only a few annotated examples in support images. Although progress has been made recently by combining prototype-based metric learning, existing methods still face two main challenges. First, various intra-class objects between the support and query images or semantically similar inter-class objects can seriously harm the segmentation performance due to their poor feature representations. Second, the latent novel classes are treated as the background in most methods, leading to a learning bias, whereby these novel classes are difficult to correctly segment as foreground. To solve these problems, we propose a dual-branch learning method. The class-specific branch encourages representations of objects to be more distinguishable by increasing the inter-class distance while decreasing the intra-class distance. In parallel, the class-agnostic branch focuses on minimizing the foreground class feature distribution and maximizing the features between the foreground and background, thus increasing the generalizability to novel classes in the test stage. Furthermore, to obtain more representative features, pixel-level and prototype-level semantic learning are both involved in the two branches. The method is evaluated on PASCAL-<inline-formula> <tex-math notation="LaTeX">$5^{i}~1$ </tex-math></inline-formula>-shot, PASCAL-<inline-formula> <tex-math notation="LaTeX">$5^{i}~5$ </tex-math></inline-formula>-shot, COCO-<inline-formula> <tex-math notation="LaTeX">$20^{i}~1$ </tex-math></inline-formula>-shot, and COCO-<inline-formula> <tex-math notation="LaTeX">$20^{i}~5$ </tex-math></inline-formula>-shot, and extensive experiments show that our approach is effective for few-shot semantic segmentation despite its simplicity.
Molecular insights into the determinants of substrate specificity and efflux inhibition of the RND efflux pumps AcrB and AdeB

Gram-negative bacterial members of the Resistance Nodulation and cell Division (RND) superfamily form tripartite efflux pump systems that span the cell envelope. One of the intriguing features of the multiple drug efflux members of this superfamily is their ability to recognize different classes of antibiotics, dyes, solvents, bile salts, and detergents. This review provides an overview of the molecular mechanisms of multiple drug efflux catalysed by the tripartite RND efflux system AcrAB-TolC from Eschericha coli. The determinants for sequential or simultaneous multiple substrate binding and efflux pump inhibitor binding are discussed. A comparison is made with the determinants for substrate binding of AdeB from Acinetobacter baumannii, which acts within the AdeABC multidrug efflux system. There is an apparent general similarity between the structures of AcrB and AdeB and their substrate specificity. However, the presence of distinct conformational states and different drug efflux capacities as revealed by single-particle cryo-EM and mutational analysis suggest that the drug binding and transport features exhibited by AcrB may not be directly extrapolated to the homolog AdeB efflux pump.
Physicochemical, Microbiological and Sensory Qualities of Milk Extract from Three Varieties of Tigernut during Storage

Tigernut milk extracted from three varieties in different locations were investigated for physicochemical, microbiological and sensory qualities during storage at ambient temperature (27±2℃). Samples were taken daily to determine the total viable count, pH, total titratable acidity, vitamin C, viscosity, reducing sugar and sensory attributes. The microbial population and load were increased over a period of time with fresh yellow tiger nut milk sample (XY) having the highest total viable mesophilic bacterial load (1.0×10 3 to 7.0× 10 4 cfu/ml), followed by Dry small brown tigernut milk sample (ZZ) with highest population of lactic acid bacteria (6.0×10 3 to 4.5× 10 4 cfu/ml) and the lowest fungal count (2.0×10 3 to 1.1× 10 4 sfu/ml), while Dry big brown tiger nut milk sample (YZ) had the highest (2.70 × 10 4 sfu/g) fungal count. Five species of microorganisms were identified. There was drop in the pH values from 4.7 to 3.6 with the increase in the percentage of total titratable acidity (TTA) from 0.49% to 1.06 % over time in all the milk samples. Viscosity at 5% of YZ milk sample was steady (1.0 Cp), while others decreased from 2.0 to 1.0 Cp. Likewise, the percentage sugar brix level of the milk samples decreased from 5.99% to 2.49% and vitamin C from 30.21 mg/ 100 mL to 20.14 mg/ 100 ml. The sensory qualities of milk sample ZZ had the best overall acceptability while the milk sample YZ was least accepted. Keyword: Tigernut milk, Storage, Physicochemical properties, Sensory evaluation, Microbial load. DOI : 10.7176/FSQM/84-06
Unveiling the Genetic Landscape of Feed Efficiency in Holstein Dairy Cows: Insights into Heritability, Genetic Markers, and Pathways via Meta-Analysis

Abstract Improving the feeding efficiency of dairy cows is a key component to improve the utilization of land resources and meet the demand for high-quality protein. Advances in genomic methods and omics techniques have made it possible to breed more efficient dairy cows through genomic selection. The aim of this review is to obtain a comprehensive understanding of the biological background of feed efficiency (FE) complex traits in purebred Holstein dairy cows including heritability estimate, and genetic markers, genes, and pathways participating in FE regulation mechanism. Through a literature search, we systematically reviewed the heritability estimation, molecular genetic markers, genes, biomarkers, and pathways of traits related to feeding efficiency in Holstein dairy cows. A meta-analysis based on a random-effects model was performed to combine reported heritability estimates of FE complex. The heritability of residual feed intake, dry matter intake, and energy balance was 0.20, 0.34, and 0.22, respectively, which proved that it was reasonable to include the related traits in the selection breeding program. For molecular genetic markers, a total of 13 single-nucleotide polymorphisms and copy number variance loci, associated genes, and functions were reported to be significant across populations. A total of 169 reported candidate genes were summarized on a large scale, using a higher threshold (adjusted P value < 0.05). Then, the subsequent pathway enrichment of these genes was performed. The important genes reported in the articles were included in a gene list and the gene list was enriched by gene ontology (GO):biological process (BP), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. Three GO:BP terms and four KEGG terms were statistically significant, which mainly focused on adenosine triphosphate (ATP) synthesis, electron transport chain, and OXPHOS pathway. Among these pathways, involved genes such as ATP5MC2, NDUFA, COX7A2, UQCR, and MMP are particularly important as they were previously reported. Twenty-nine reported biological mechanisms along with involved genes were explained mainly by four biological pathways (insulin-like growth factor axis, lipid metabolism, oxidative phosphorylation pathways, tryptophan metabolism). The information from this study will be useful for future studies of genomic selection breeding and genetic structures influencing animal FE. A better understanding of the underlying biological mechanisms would be beneficial, particularly as it might address genetic antagonism.