Miracle-dz/UniFAR-FTUs huggingface dataset:
A multifunctional silk coating on additively manufactured porous titanium to prevent implant-associated infection and stimulate bone regeneration

Despite tremendous progress in the design and manufacturing of metallic implants, they do not outlive the patient. To illustrate, more than half of hip replacements will fail, mainly due to implant infection and loosening. Surface engineering approaches and, in particular, coatings can facilitate implant bio-functionality via the recruitment of more host cells for new bone formation and inhibition of bacterial colonization. Here, we used electrophoretic deposition to apply a silk fibroin solution consisting of tricalcium phosphate (TCP) and vancomycin as a coating on the surface of additively-manufactured porous titanium. Furthermore, the surface properties of the coatings developed and the release kinetics of the vancomycin were studied to evaluate the applied coating. The in vitro antibacterial behavior of the multifunctional coating, as well as the cell viability and osteogenic differentiation of the MC3T3-E1 cell line were extensively studied. The biomaterials developed exhibited an antibacterial behavior with a reduction of up to four orders of magnitude in both planktonic and adherent bacteria for 6 h and 1 d. A live-dead assay, the Alamar Blue activity, the DNA content, and cytoskeleton staining demonstrated a significant increase in the cell density of the coated groups versus the as-manufactured ones. The significantly enhanced calcium deposition and the increase in mineralization for the groups with TCP after 21 and 28 d, respectively, demonstrate upregulation of the MC3T3 cells’ osteogenic differentiation. Our results collectively show that the multifunctional coating studied here can be potentially used to develop a new generation of orthopedic implants.
Reproducibility of radiomics features derived from intravoxel incoherent motion diffusion-weighted MRI of cervical cancer

Background The reproducibility of intravoxel incoherent motion (IVIM)-based radiomics studies in humans has not been reported. Purpose To determine the inter- and intra-observer variability on the reproducibility of IVIM-based radiomics features in cervical cancer (CC). Material and Methods The IVIM images of 25 patients with CC were retrospectively collected. Based on the high-resolution T2-weighted images, the regions of interest (ROIs) were independently delineated twice in diffusion-weighted images at a b value of 1000 s/mm2 (interval time was one month) by two radiologists. This was done at the largest transversal cross-sections of the tumors. The ROI was subsequently used in apparent diffusion coefficient (ADC), true diffusion coefficient (D), pseudo-diffusion coefficient (D*), and perfusion fraction (f) maps derived from IVIM images. In total, 105 radiomics features were then finally extracted from the IVIM-derived maps. The inter- and intra-observer reproducibility of IVIM-derived features was then evaluated using the intraclass correlation coefficient. Results Inter- and intra-observer variability affected the reproducibility of radiomics features. D* map had 100% and 95% reproducible features, ADC map had 89% and 93%, D map had 97% and 86%, while f map had 54% and 62% reproducible features with good to excellent reliability in the intra-observer analysis. Similarly, D* map had 90% and 94%, ADC map had 85% and 70%, D map had 81% and 78%, while f map had 41% and 93% reproducible features with good to excellent reliability in the inter-observer analysis. Conclusion Inter- and intra-observer variability can affect radiomics analysis. Cognizant to this, multicenter studies should pay more attention to intra- and inter-observer variability.
Analysis of genetic diversity of chickpea cultivars using STMS markers

A set of 38 chickpea cultivars were assessed in this study at the molecular level using 8 STMS (Sequence-Tagged Microsatellite Site) markers. This set includes advanced lines from the Tunisian breeding program, Tunisian varieties and reference lines from ICARDA (International Centre for Agricultural Research in Dry Areas, ICRISAT (International Crops Research Institute for the Semi-Arid-Tropics) and other countries. A total of 58 alleles were generated from the amplification of the 8 microsatellite sites studied with an average value of 7.25 alleles per locus, which explain a high level of polymorphism within the cultivars studied. All the cultivars studied showed a unique genetic profile, each one using the genotypic combination of all loci studied. Only three STMS markers (TA59, TA64, and TA71) from the eight studied showed the highest number of alleles, the effective number of alleles and the highest values of power of discrimination allow us the unambiguous discrimination of all the cultivars studied. The Dice coefficient of similarity was calculated between all pairs of accessions and UPGMA analysis was performed from the genetic similarity matrix, and allowed the arrangement of all genotypes according to their genetic relationships. The genetic similarity among cultivars observed in this work, led to their separation according to their pedigree, their morphological characteristics and their environment adaptation for biotic and abiotic stresses. The results of this work suggest that microsatellite markers are valuable tools for molecular characterization and analysis of diversity in chickpea.
Contribution du régulon sigma B à la pathogenèse de variants de STAPHYLOCOCCUS AUREUS formant de petites colonies lors d'infections pulmonaires chroniques chez les patients atteints de fibrose kystique

Staphylococcus aureus small-colony variants (SCVs) and biofilms are linked to chronic infections. It is known that the presence of aminoglycoside antibiotics may contribute to the emergence of SCVs and it is thought that molecular mechanisms are involved in the ability of S. aureus to adopt this phenotype. No study has addressed the possible role of the stressand colonization-related alternative sigma factor B (SigB) in the emergence of SCVs, although a sustained SigB activity was reported in these variants. Here, we demonstrate that SigB is involved in the emergence of SCVs resulting from an exposure to a sub-inhibitory concentration of aminoglycosides. Monitoring of gene expression in an aminoglycosidetreated prototypical strain or in clinical SCVs showed the activation of SigB, whereas the accessory gene regulator {agr) system was not. Furthermore, gentamicin-treated prototypical bacteria and SCVs had an increased ability to form biofilm only in a SigB functional background. The administration of a sub-inhibitory concentration of gentamicin significantly increased the formation of SCVs for a prototypical strain but not for the sigB mutant in a mouse model of S. awrews-induced mastitis. Collectively, our results show that SigB may positively influence the appearance of S. aureus SCVs and the production of biofilm upon aminoglycoside exposure.
THE EFFECT OF DRY CAPER (Capparis spinosa) FRUIT ON EGG PRODUCTION AND QUALITY CHARACTERISTICS OF LAYING HENS

This study was conducted to determine the effect of increasing dietary inclusion of dry Caper (Capparis spinosa) fruit (DCF) on egg production and quality characteristics of laying hens between 20 and 32 weeks of age. Four groups of commercial hens (ATAK-S) were fed with diets containing 0, 5, 10 and 15 g DCF/kg. The results showed that final body weight, feed intake, shape index (SI) and morning hen–day egg yield were influenced by dietary supplementation of DCF (P 0.05) during the entire experiment. The lightness (L*) and redness (a*) values for egg shell color were similar (P>0.05) in the DCL supplemented groups as compared to the control group. The yellowness (b*), Hue angle (H), chroma (C*) and ∆E* values were lower (P<0.05) in 15 g DFC/kg group when compared with the control. Trolox equivalent antioxidant capacity (TEAC), ferric reducing antioxidant power (FRAP) and total phenolics amount of DCF were 43.75±0.680 mmol trolox/kg, 60.03±3.710 mmol TEAC/kg and 3.16±0.060 g gallic acid equivalents (GAE)/kg, respectively. Based on the results from the current study, the dietary supplementation with dry DCF had adverse effects on productivity performance traits and egg quality.
A functional role for eicosanoid-lysophospholipids in activating monocyte signaling

Recently, eicosanoid-lysophospholipids were identified as novel metabolites generated from the direct cyclooxygenase- or lipoxygenase-catalyzed oxidation of 2-arachidonoyl-lysophospholipids produced from either phospholipase A1-mediated hydrolysis of diacyl arachidonoyl-phospholipids or through the cytochrome c-catalyzed oxidative hydrolysis of the vinyl ether linkage of arachidonoyl-plasmalogens. Although the metabolic pathways generating eicosanoid-lysophospholipids have been increasingly appreciated, the signaling functions of eicosanoid-lysophospholipids remain largely unknown. Herein, we demonstrate that 2-12(S)-HETE-lysophospholipids as well as nonesterified 12(S)-HETE are potent lipid mediators that activate THP-1 human monocytic cells to generate tumor necrosis factor α (TNFα) and interleukin 8 (IL8). Remarkably, low nanomolar concentrations of 12(S)-HETE-lysophospholipids, but not other oxidized signaling lipids examined activated THP-1 cells resulting in the production of large amounts of TNFα. Moreover, TNFα release induced by 12(S)-HETE-lysophospholipids was inhibited by the TNFα converting enzyme inhibitor TAPI-0 indicating normal processing of TNFα in THP-1 cells stimulated with these agonists. Western blotting analyses revealed that 12(S)-HETE-lysophospholipids activated the phosphorylation of NFκB p65, suggesting activation of the canonical NFκB signaling pathway. Importantly, activation of THP-1 cells to release TNFα was stereoselective with 12(S)-HETE favored over 12(R)-HETE. Furthermore, the EC50 of 2-12(S)-HETE-lysophosphatidylcholine in activating THP-1 cells was 2.1 nm, whereas the EC50 of free 12(S)-HETE was 23 nm. Additionally, lipid extracts of activated platelets were separated by RP-HPLC demonstrating the coelution of 12(S)-HETE with fractions initiating TNFα release. Collectively, these results demonstrate the potent signaling properties of 2-12(S)-HETE-lysophospholipids and 12(S)-HETE by their ability to release TNFα and activate NFκB signaling thereby revealing a previously unknown role of 2-12(S)-HETE-lysophospholipids in mediating inflammatory responses.
Metabolomics study of human embryonic stem cell culture media

Self-renewal and pluripotency, the hallmarks of human embryonic stem cells (hESC), confer these cells with the capacity to expand indefinitely while maintaining the ability to differentiate into any cell type of the human body; thus, making hESC a valuable source of functional differentiated cells suitable for applications in regenerative medicine, drug discovery, biotechnology, biopharmaceuticals and developmental biology. However, the large-scale production of clinical-grade hESC, required for such applications, has been hampered by the current culture conditions in which hESC still depend on the use of mouse embryonic fibroblast-conditioned medium (MEF-CM) for their efficient growth. Therefore, investigation of the factors provided by MEFs is of the utmost importance to discover which components of MEF-CM allow the long-term expansion of undifferentiated hESC. While considerable progress has been made on the identification of the protein components of MEF-CM, very little is known about the small molecules (metabolites) secreted by MEFs. In this context, an untargeted metabolomics method was developed for the investigation of potential bioactive metabolites present in MEF-CM implicated in the proliferation and/or maintenance of pluripotency of hESC in vitro. A metabolomics method was applied and successfully identified a number of metabolites which were later confirmed in their identities with the use of authentic standards, to be further investigated for their effect on hESC culture. Interestingly, the addition of PGE2, 6-keto-PGF1α, 9, 12, 13-TriHOME, 7-Ketocholesterol and stearidonic acid (the metabolites found in MEF-CM) to the unconditioned medium (UM), a medium incapable of the maintenance of hESC, showed a delay in apoptosis when compared to the negative control UM; thus, suggesting that these metabolites could help with the proliferation of hESC. Increasing evidence that hESC secrete factors into their microenvironment that can also help them to proliferate or to maintain an undifferentiated state prompted the application of the same metabolomics method to the analysis of hESC spent culture media. The results identified lysophospholipids (LPLs) as potential molecules mediating some biological activities; however, the precise role of these LPLs still remains to be determined. Overall, the results of this thesis are expected to impact and add knowledge to the field of stem cell biology providing useful information for the creation and development of more efficient and defined culture conditions for the propagation of hESC with the appropriate quality to realise their widespread application in clinic and other research areas.
Can migrants escape from density dependence

Migration is thought to maximize growth by enabling individuals to escape from density dependence, but this has rarely been tested at the individual level in natural populations. We employed linear mixed modeling of the spacing between consecutive scale growth rings to reconstruct individual growth profiles of a paradigmatic fish migrant, the sea trout (Salmo trutta) and related these to estimates of year class strength over a 13-year period. Variation in scale growth was 1.3 times greater among individuals than within individuals in freshwater and 10 times greater at sea. Scale growth was inversely related to year class strength, both in freshwater (before migration) and at sea (after migration). Competition for patchily distributed resources is the most plausible explanation of the negative density-dependent growth observed in freshwater and, to a lesser extent, in the marine environment. Our study provides some of the strongest evidence for a role of density dependence in determining partial migrations because although migrants can maximize growth by moving into the sea, they do not appear to become free from density dependence constraints completely. This has implications for conservation and suggests that sea trout and other anadromous fish displaying partial migrations may not be best managed on a river by river basis, but rather from a broader, coastal perspective.
Insight into the sequence-structure relationship of TLR cytoplasm’s Toll/Interleukin-1 receptor domain towards understanding the conserved functionality of TLR 2 heterodimer in mammals

Abstract The signaling response of TLR2 to ligands has always been as a homodimer or in heterodimerization with TLR1/TLR6. The Toll/Interleukin-1 Receptor (TIR) domain of the TLR cytoplasmic region regulates the dimerization and interactions with adaptor molecules to build an active signaling complex. To understand the conservation of functionality of the TLR2-heterodimers between the distantly related species human(h) and mice(m), the pattern of TIR-TIR interaction in heterodimers has been studied through the sequence-structural point of view. Comparative analysis of primary sequence and structural pattern of TLRs(1/2/6) corroborates higher sequence homology between TLR1 and TLR6. Molecular docking analysis of TLR2-TLR1 and TLR2-TLR6 cytoplasmic dimers in both mouse and human have identified that for interaction the BB loop/near-BB loop residues of TLR2 are involved with the near-DD loop of TLR1 and DD loop residues of TLR6 within the TIR domains, which may cause to differential signaling. Molecular dynamics simulation of dimers for both human and mice species recognize stable interface between near-BB/BB loop region of TLR2 and discrete near-DD and DD loop region of TLR1 and TLR6 respectively. The observed dimerization pattern in both the species is further supported by Alanine scanning mutation study. However, Solvent Accessible Surface Area (SASA) of BB and DD loop regions of the cytoplasmic monomers and the heterodimers suggests that while TLR2 BB loop is actively associated as the dimer interface with its heterodimer partners in both the species, the DD loop acts as the active interfacing region in hTLR1 and mTLR6. Communicated by Ramaswamy H. Sarma
A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.
Estimation of in vitro methane production in buffalo and cow.

The greenhouse effect of methane (CH4) has been considered high compared to the other green house gases (GHG), thought to be around 20 times that of carbon dioxide. The methane production from enteric fermentation in animal agriculture contributes around 20% of the total global methane. Several studies on methane production from ruminants have been effected but few is known on buffalo, even if buffalo is considered potentially the most serious methane contributor for its better utilization of low quality feedstuffs than cattle This study was carried out to compare the methane production by buffalo and bovine by the in vitro gas production technique, using three forages (corn silage, grass silage, wheat straw). As inocula rumen fluid collected from fistulated buffalo and bovine were used. Acetic, propionic and butyric acids, produced after 120 hours of incubation, were utilised to estimate CH4 production. The total gas and the total volatile fatty acids production were consistently higher for bovine compared with buffalo (OMCV: 336 vs. 276 ml/g, P<0.001 and tVFA: 88.5 vs. 81.8 mM/g, P<0.01 in dairy cow and buffalo, respectively), although organic matter degradability was the same for both inocula (dOM: 70.0 vs. 69.3 %). The average CH4 produced in vitro with buffalo inoculum was always lower, either when related to the degraded organic matter (75.1 vs. 97.1 ml/g; P<0.001), or when reported as % of total gas (18.8 vs. 20.3).
tasiR-ARFs Production and Target Regulation during In Vitro Maize Plant Regeneration

During in vitro maize plant regeneration somatic cells change their normal fate and undergo restructuring to generate pluripotent cells able to originate new plants. Auxins are essential to achieve such plasticity. Their physiological effects are mediated by auxin response factors (ARFs) that bind auxin responsive elements within gene promoters. Small trans-acting (ta)-siRNAs, originated from miR390-guided TAS3 primary transcript cleavage, target ARF3/4 class (tasiR-ARFs). Here we found that TAS3b precursor as well as derived tasiR-ARFbD5 and tasiR-ARFbD6 display significantly lower levels in non-embryogenic callus (NEC), while TAS3g, miR390 and tasiR-ARFg are more abundant in the same tissue. However, Argonaute (AGO7) and leafbladeless 1 (LBLl) required for tasiR-ARF biogenesis showed significantly higher transcript levels in EC suggesting limited tasiR-ARF biogenesis in NEC. The five maize ARFs targeted by tasiR-ARFs were also significantly enriched in EC and accompanied by higher auxin accumulation with punctuate patterns in this tissue. At hormone half-reduction and photoperiod implementation, plant regeneration initiated from EC with transient TAS3g, miR390 and tasiR-ARFg increase. Upon complete hormone depletion, TAS3b became abundant and derived tasiR-ARFs gradually increased at further regeneration stages. ZmARF transcripts targeted by tasiR-ARFs, as well as AGO7 and LBL1 showed significantly lower levels during regeneration than in EC. These results indicate a dynamic tasiR-ARF mediated regulation throughout maize in vitro plant regeneration.
Analysis of CRISPR/Cas9 guide RNA efficiency and specificity against genetically diverse HIV-1 isolates.

Gene editing approaches using CRISPR/Cas9 are being developed as a means for targeting the integrated HIV-1 provirus. Enthusiasm for the use of gene editing as an anti-HIV-1 therapeutic has been tempered by concerns about the specificity and efficacy of this approach. Guide RNAs (gRNAs) that target conserved sequences across a wide range of genetically diverse HIV-1 isolates will have greater clinical utility. However, on-target efficacy should be considered in the context of off-target cleavage events as these may comprise an essential safety parameter for CRISPR-based therapeutics. We analyzed a panel of Streptococcus pyogenes Cas9 (SpCas9) gRNAs directed to the 5' and 3' long terminal repeat (LTR) regions of HIV-1. We used in vitro cleavage assays with genetically diverse HIV-1 LTR sequences to determine gRNA activity across HIV-1 clades. Lipid-based transfection of gRNA/Cas9 ribonucleoproteins (RNPs) was used to assess targeting of the integrated HIV-1 proviral sequence in cells (in vivo). For both the in vitro and in vivo experiments, we observed increased efficiency of sequence disruption through the simultaneous use of two distinct gRNAs. Next, CIRCLE-Seq was utilized to identify off-target cleavage events using genomic DNA from cells with integrated HIV-1 proviral DNA. We identified a guide RNA targeting the U3 region of the LTR (termed SpCas9-127HBX2) with broad cleavage efficiency against sequences from genetically diverse HIV-1 strains. Based on these results, we propose a workflow for identification and development of anti-HIV CRISPR therapeutics.
Prevalence of endo‐ and ecto‐parasites of equines in Iran: A systematic review

Abstract Equines are subject to infection with many parasites, which threaten their health. In the present study, we systematically reviewed existing literature on the prevalence of endo‐ and ectoparasites of equines in Iran. Major electronic databases, including PubMed, PubMed Central, Google Scholar, Science Direct and Scientific Information Database (SID), were searched (Last updated 11/05/2018) for relevant literature of parasites that have been identified from equines in Iran. Of the 1809 titles produced by bibliographic search, 38 were included in the review. Twenty‐seven of the studies were on horses, six on donkeys, three on both horses and donkeys, and one study was on both horses and mules. Furthermore, 24 of the studies reported infections caused by protozoa, thirteen by helminths, two by ectoparasites, and one by both protozoa and helminths. The overall pooled prevalence of parasitic infection was 28.8% (95%CI: 22.9–35.7, I 2 = 93.4%). Helminths were the most prevalent parasites 46.7% (95% CI: 24.1–70.7, I 2 = 96.0%). Furthermore, donkeys were the most affected equine, with a prevalence of 70.7% (95% CI: 53.2–83.7, I 2 = 92.5%). The protozoa frequently reported included nine species belonging to the genera: Neospora, Toxoplasma, Theileria, Babesia and Eimeria. Also, the helminths frequently reported included 21 species belonging to the genera: Strongylus, Dicrocoelium, Oxyuris, Habronema, Echinococcus, Dictyocaulus, Cyathostomum, Probstmayria, Anoplocephala, Setaria and Fasciola. Ticks were the only ectoparasites frequently reported. Parasitic fly species of the genera Gasterophilus were also reported. The study‐level risk of bias was likely to be high because of differences in study design. Parasitic infections of equines in Iran are frequent and caused by a diversity of parasites, which threatens the health and well‐being of these animals. Further research is needed in the area to identify the risk factors of infection for effective control of the parasites.