Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the molecular mechanism of the anti-atherosclerotic effect of policosanol in atherosclerosis rat

Objective:To characterize the anti-atherosclerotic molecular mechanism of policosanol in atherosclerosis rat.Rat atherosclerosis model was prepared by intraperitoneal injection of vitamin D3 with high cholesterol diet for 12 weeks.Methods:Forty SD rats were randomly divided into four groups:the normal group,atherosclerosis(AS) group,atorvastatin group and policosanol group.Serum lipids and serum inflammatory cytokine hs-CRP were detected enzymatically(end-point method /CHO-PAP method) and ELISA method,respectively.The atherosclerosis of the abdominal aorta was observed under an electron microscope.The expression of p-p38MAPK was analyzed by Western blot.Results:The normal group showed intact endothelium.AS formations were significantly greater in the AS group.The serum lipid levels,the content of serum inflammatory cytokines hs-CRP and the expression of pp38MAPK in the policosanol group were between the AS group and the normal group,which were the highest in the AS group.Conclusion:Apart from its lipid-lowering effects,policosanol reduced the production of serum hs-CRP and inhibited the expression of p-p38MAPK in AS rats.The p38MAPK phosphorylation pathway may be involved in the anti-atherosclerosis molecular mechanism of policosanol in AS rats.
Sparsity of Protein-Protein Interaction Networks Hinders Function Prediction in Non-Model Species

Motivation Physical interaction between two proteins is strong evidence that the proteins are involved in the same biological process, making Protein-Protein Interaction (PPI) networks a valuable data resource for predicting the cellular functions of proteins. However, PPI networks are largely incomplete for non-model species. Here, we test whether these incomplete networks are still useful for genome-wide function prediction. Results We used a simple network-based classifier to predict Biological Process Gene Ontology terms from protein interaction data in three species: Saccharomyces cerevisiae, Arabidopsis thaliana and Solanum lycopersicum (tomato). The classifier had reasonable performance in the well-studied yeast, but performed poorly in the other two species. We show that this poor performance is because many proteins are disconnected in the network and that the performance can be considerably improved by adding edges predicted from various data sources. In yeast, the addition of predicted edges did not lead to improvement. It did help when we randomly removed a large amount of edges though. Conclusion Our work highlights the necessity of obtaining more protein-protein interactions in non-model species, either by means of prediction or experiment. Availability Data and code to reproduce the results are available at github.com/stamakro/ppi-missing-data. Contact s.makrodimitris@tudelft.nl Supplementary information Supplementary data are available online.
Genetic Diversification and Selection Strategies for Improving Sorghum Grain Yield Under Phosphorous-Deficient Conditions in West Africa

Sorghum, a major crop for income generation and food security in West and Central Africa, is predominantly grown in low-input farming systems with serious soil phosphorus (P) deficiencies. This study (a) estimates genetic parameters needed to design selection protocols that optimize genetic gains for yield under low-phosphorus conditions and (b) examines the utility of introgressed backcross nested association mapping (BCNAM) populations for diversifying Malian breeding materials. A total of 1083 BC1F5 progenies derived from an elite hybrid restorer “Lata-3” and 13 diverse donor accessions were evaluated for yield and agronomic traits under contrasting soil P conditions in Mali in 2013. A subset of 298 progenies were further tested under low-P (LP) and high-P (HP) conditions in 2014 and 2015. Significant genetic variation for grain yield was observed under LP and HP conditions. Selection for grain yield under LP conditions was feasible and more efficient than the indirect selection under HP in all three years of testing. Several of the BCNAM populations exhibited yields under LP conditions that were superior to the elite restorer line used as a recurrent parent. The BCNAM approach appears promising for diversifying the male parent pool with introgression of diverse materials using both adapted Malian breed and unadapted landrace material from distant geographic origins as donors.
PCA-based source-space contrast maps reveal psychologically meaningful individual differences in continuous MEG activity

Within the field of neuroimaging, there has been an increasing trend towards studying brain activity in naturalistic conditions, and it is possible to robustly estimate networks of on-going oscillatory activity in the brain. However, not many studies have focused on differences between individuals in on-going brain activity that would be associable to psychological or behavioral characteristics. Existing standard methods can perform well at single-participant level, but generalizing the methodology across many participants is challenging due to individual differences of brains. As an example of a clinically relevant, naturalistic condition we consider here mindfulness. Trait mindfulness, as well as a mindfulness-based intervention cultivating focused attention, is often associated with benefits for psychological health. Therefore, the manner in which the brain engages in focused attention vs. mind wandering is likely to associate with individual differences in psycho–behavioral tendencies. We recorded MEG from 29 participants both in a state of focused attention and in a state of simulated mind wandering. We used Principal Component Analysis to decompose spatial average activation maps of focused attention contrasted with two different mind wandering states. The first principal component, which reflected differential engagement of bilateral parietal areas during focused attention vs. mind wandering, was associated with behavioral characteristics of inhibition, anxiousness and depression, as measured by standard questionnaires. We demonstrated that such decomposition of time-averaged contrast maps can overcome some of the challenges in methods based on concatenated data, especially from the perspective of behaviorally and clinically relevant characteristics in the ongoing brain oscillatory activity. Highlights We present a specific method to analyse/establish associations between brain oscillations and behavioral characteristics. We found that activity levels in parietal areas during mind wandering compared to focused attention were associated with the behavioral trait of inhibition and anxiety.
A/T/N polygenic risk score for cognitive decline in old age

INTRODUCTION We developed a novel polygenic risk score (PRS) based on the A/T/N (amyloid plaques (A), phosphorylated tau tangles (T), and neurodegeneration (N)) framework and compared a PRS based on clinical AD diagnosis to assess which was a better predictor of cognitive decline. METHODS We used summary statistics from genome wide association studies of cerebrospinal fluid amyloid-β (Aβ42) and phosphorylated-tau (ptau181), left hippocampal volume (LHIPV), and late-onset AD dementia to calculate PRS for 1181 participants in the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Individual PRS were averaged to generate a composite A/T/N PRS. We assessed the association of PRS with baseline and longitudinal cognitive composites of executive function and memory. RESULTS The A/T/N PRS showed superior predictive performance on AD biomarkers and executive function decline compared to the clinical AD PRS. DISCUSSION Results suggest that integration of genetic risk across AD biomarkers may improve prediction of disease progression. Research in Context Systematic Review Authors reviewed relevant literature using PubMed and Google Scholar. Key studies that generated and validated polygenic risk scores (PRS) for clinical and pathologic AD were cited. PRS scores have been increasingly used in the literature but clinical utility continues to be questioned. Interpretation In the current research landscape concerning PRS clinical utility in the AD space, there is room for model improvement and our hypothesis was that a PRS with integrated risk for AD biomarkers could yield a better model for cognitive decline. Future Directions This study serves as proof-of-concept that encourages future study of integrated PRS across disease markers and utility in taking an A/T/N (amyloidosis, tauopathy and neurodegeneration) focused approach to genetic risk for cognitive decline and AD.
Homeostatic regulation of dissolved labile organic substrates by consumption and release processes in a freshwater lake

We examined short‐term changes and spatial variability of dissolved free amino acids (DFAA) and glucose in mesotrophic Lake Zurich (Switzerland) at 2‐ to 4‐day intervals over 5 weeks during spring. Heterotrophic incorporation, consumption (“gross” uptake), and release of free leucine and glucose were assessed using isotopically labeled tracers. Glucose exhibited significantly higher consumption and release rates but a lower turnover time than leucine. The net uptake, release, and turnover time of both substrates were significantly correlated, suggesting that their microbial processing was closely coupled. Net changes of individual DFAA and glucose during dark short‐term incubations with unfiltered samples including phytoplankton were conspicuously similar, indicating that bulk heterotrophic consumption of labile substrates was nonselective and depended primarily on their availability. Changes of DFAA during incubations were significantly related to their initial concentrations. Specifically, DFAA concentrations tended to converge toward their seasonal in situ median concentrations, which likely represented the balanced state of net release vs. consumption. There was a clear difference between relatively stable compounds (glucose, leucine, arginine) and others that showed pronounced concentration changes during incubations (alanine, valine, glycine), pointing to a variable degree of uncoupling between consumption and release. Moreover, short‐term changes of DFAA concentrations in incubations were also related to their variability in replicate 5‐liter samples taken from the lake, suggesting that biological processes such as consumption and release may influence the mesoscale spatial distribution of DFAA in the epilimnion of a lake. Overall, we document the homeostatic regulation of labile dissolved substrates by varying release and consumption processes.
Molecular Evolution of the Sex Peptide Network in Drosophila

Successful reproduction depends on interactions between numerous proteins beyond those involved directly in gamete fusion. While such reproductive proteins evolve in response to sexual selection pressures, how networks of interacting proteins arise and evolve as reproductive phenotypes change remains an open question. Here, we investigated the molecular evolution of the “sex peptide network” of Drosophila melanogaster, a functionally well-characterized reproductive protein network. In this species, the peptide hormone sex peptide (SP) and its interacting proteins cause major changes in female physiology and behavior after mating. In contrast, females of more distantly related Drosophila species do not respond to SP. In spite of these phenotypic differences, we detected orthologs of all network proteins across 22 diverse Drosophila species and found evidence that most orthologs likely function in reproduction throughout the genus. In D. melanogaster and closely related species that show similar responses to SP, we detected the recurrent, adaptive evolution of several network proteins, consistent with sexual selection acting to continually refine network function. We also found some evidence for adaptive evolution of several proteins along two key branches of the Drosophila phylogeny on which major changes in SP-related phenotypes likely occurred. Finally, we used gene expression profiling to examine the likely degree of functional conservation of the paralogs of an SP network protein that arose via gene duplication. Our results suggest a dynamic history for the SP network in which network members arose before the onset of robust SP-mediated responses and then were shaped by both purifying and positive selection.
Molecular Identification and Virulence Factors Determination in Candida Species Isolated from Egyptian Patients

Candida-related infections are becoming a universal threat to the health of human who undergo immunosuppressive therapy or aggressive medical intervention. Objectives: The aim was to study the distribution of Candida species among winter and summer seasons and to determine the expression of their virulence factors. Methods: A total of 164 Candida isolates were collected from clinical specimens at Mansoura University Hospitals. Candida species were identified by polymerase chain reaction (PCR). Extracellular phospholipase, secretory aspartyl proteinase (SAP) and coagulase enzymes and biofilm formation were determined. SAP 9 and 10 genes were detected by PCR. Results: Non-albicans (NAC) isolates were more dominant than C. albicans isolates (P value < 0.0001). C. tropicalis was the most prevalent (59.2%) followed by C. albicans (31.1%), then C. glabrata, C. krusie, unidentified NAC and C. kefyr in 3.7%, 2.4%, 2.4% and 1.2% respectively. Extracellular phospholipase activity was detected in 31.7% of Candida isolates. All C. albicans had phospholipase activity (100%) and one isolate of C. tropicalis was positive while other species were negative. SAPs activities were determined in 61.6% of Candida isolates and were detected in 70.1% and 62.7% among C. tropicalis and C. albicans isolates respectively. SAP9 and SAP 10 genes were detected in 27.7% and 12.9% of Candida isolates showed positive SAPs activity respectively and they were all C. albicans strains. Other species did not harbor either SAP9 or SAP10. Coagulase activity was detected in 80.4% of Candida isolates with higher activity in C. albicans (88.2%), followed by C. tropicalis (81.4%), then other NAC isolates. Biofilm formation was determined in 69.5% of Candida isolates and was more prevalent in C. tropicalis (82.5%) followed by C. albicans (19.6%), C. krusie (100%), unidentified NAC (75%), C. glabrata (33.3%) and C. kefyr (50%). Conclusion: NAC with a preponderance of C. tropicalis was the most common isolated Candida species. Biofilm production, proteinase, phospholipases and coagulase enzymes were observed in both C. albicans and NAC. SAP9 and SAP 10 genes were detected only in C. albicans strains.
Age‐related ultrastructural features of the tongue of the rock pigeon Columba livia dakhlae in different three age stages (young, mature, and adult) captured from Egypt

This study represents the first attempt to describe the ultra‐structural and histological features of different three age‐stages (young, mature, and adult) of rock pigeon Columba livia dakhlae captured from Egypt. The elongated tongue with round lingual apex carried a lingual nail rostrally on lingual tip. The current work gave a first record of numerous descriptions as in young and mature, small lingual nail formed from aggregation of lingual scales, but in adult, the nail formed from lingual membrane without any lingual scales. The current work gave full descriptive methods of shape, directions, and distribution of filiform‐like papillae with lingual scales among three age‐stages on dorsal surface and lateral border of apex and body. The taste buds present only on the tongue of mature and adult pigeon. The only one transverse row in young took the wide V‐shape but, wide U‐shape in mature and adult. The papillae on the papillary crest took triangular spoonful‐like shape in young and mature, but in adult take the shape of blunt tubercles. The current work was the first record of the presence of the openings of lingual glands on concave dorsal lingual surface of giant papillae and papillae of papillary crest in adult stage. The lingual membrane was thin one membrane in young and three to four layers in mature but, in adult it is well‐developed and formed from 10–11 layers. The supportive entoglossum cartilaginous was extended rostrally till the apical part.
The curative effect on Leflunomide combined with total glucosides of peony in the treatment of ankylosing spondylitis

Objective To know the curative effect on leflunomide combined with total glucosides of peony in the treatment of ankylosing spondylitis.Methods Sixty-eight patients were randomly divided into the observed group(n = 34) and the con trol group(n = 34). The patients in the observed group accepted the treatment of leflunomide and total glucosides of peony,but the control group received the treatment of leflunomide only.The curative effect was evaluated by the Bath AS disease activity index(BASDAI),visual analogue scale(VAS) and ESR after treatment of 3 months,6 months and 12 months.Results After treatment of 3 months,the BASDI and ESR in the observed group significantly lower than that in the control group(P 0.05). After treatment of 6 months and 12 months,the BASDI,VAS and ESR in the observed group significantly lower than that in the control group,too(P 0.05). Conclusion Leflunomide combined with total glucosides of peony could get better curative effect in the treatment of ankylosing spondylitis.
Biochemical analysis of cyanobacterial strains isolated from different Tunisian inland waters: therapeutical and nutritional potential

The last decade period has been characterized by a remarkable increase in the need for food, bioenergy, and pharmaceutical compounds. Meanwhile, microalgae have been in the center of interest as a rich and sustainable source of highly valuable natural products and bioactive compounds. In this perspective, the present study aimed at investigating the biochemical composition of 10 cyanobacterial strains collected from several Tunisian inland waters, seeking to identify the possible use of cyanobacteria in nutraceuticals and pharmaceuticals industry, and for animal and human consumption. Ten local strains of cyanobacteria were isolated from several Tunisian inland waters and cultured in controlled laboratory conditions. Fatty Acid methyl esters were analyzed in each strain by Gas chromatography–Mass spectrometry (GC-MS) as well as total proteins, carbohydrates and different phycobiliproteins (phycocyanin, allophycocyanin and phycoerythrin). Results showed that Planktothrix agardhii, Leptolyngbya sp1. , and Leptolyngbya sp2. contained 14 different fatty acids, among which oleic acid was the most abundant. These might be important in nutraceutical and agronomic sectors due to the potent antioxidant and larvicidal activities of oleic acid. Cylindrospermopsis raciborskii presents extraordinarily high levels of phycocyanin, making it an exceptional natural reservoir of effective and non-toxic drugs that are of particular interest against cancer and neurodegenerative diseases. Extracts from cyanobacterial strains represent a natural and available source of proteins, of highly valuable fatty acids, and especially of phycocyanin which is known by its extremely health beneficial properties. The nutritional and functional complements provided by these extracts can be used in the prevention of various diseases and also as effective and environmentally friendly insecticides. © 2019 International Formulae Group. All rights reserved.Keywords: Cyanobacteria; biochemical composition; fatty acids; phycobiliproteins; valorization
Frequency and synchronisation features of a highly overlapped duet changes according to the context

ABSTRACT Territorial defence and maintaining contact are two hypotheses of duet functions. Nevertheless, the acoustic characteristics of duets in these contexts have been poorly quantified. This work aimed to compare the spectrotemporal characteristics and synchronisation in White-eared Ground-sparrow duets produced in aggressive context (i.e. territorial defence) and non-aggressive context (i.e. pair-contact). We expected to observe differences when compare duets of the same pair in each context. For this, we recorded 35 pairs in each context: territorial defence and pair-contact. We measured duration, minimum, highest, and maximum amplitude frequency. Synchronisation was measured comparing time and frequency bandwidth variation in three sections of duets produced in both contexts. In territory defence contexts, duets showed lower minimum frequencies and were produced with lower frequency synchronisation between first and middle section bandwidth; but with higher frequency synchronisation between middle and final section bandwidth. This suggests that this ground-sparrow encode context-depend information changing the frequency characteristics of duets. For example, to decrease the minimum frequency on the duets produced in territorial defence context could be understood as a most aggressive signal to the intruder, because in several species low-frequency sounds are associated with higher probability to attack the intruders or with larger and dominant individuals.
Non-coding rather than coding regions underpin avian bill shape diversification at macroevolutionary scales

Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We design a novel approach by integrating class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 non-coding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified non-coding regions are involved in craniofacial embryo development in mammals. We identify two associated pathways, BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This result suggests that our approach identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and non-coding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to non-coding loci. Moreover we find evidence for signatures of recent diversifying selection in the identified non-coding loci in populations of Darwin’s finches that differ notably in their beak shape morphology. Our results suggest that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.