Miracle-dz/UniFAR-FTUs huggingface dataset:
Amanita cingulata, a new annulate species of Amanita sect. Vaginatae from subtropical China

Amanita cingulata , a new species of Amanita sect. Vaginatae with an annulus on the stipe is described based on morphological and molecular evidence. This species was found in forests dominated by members of Fagaceae and/or Pinaceae and is characterized by its small basidioma with a white pileus covered with white and lumpy volval remnants, a pileal margin with short striations, a white fragile annulus, a weak and easily broken lumpy volva on the stipe base and ellipsoid to elongate basidiospores measuring 9–11.5 × 5.5–7 μm. The new species is compared with similar species, especially the annulate taxa of A. sect. Vaginatae.
Antagonism between Byssochlamys spectabilis (anamorph Paecilomyces variotii) and plant pathogens: Involvement of the bioactive compounds produced by the endophyte

Fungal endophytes can be part of the defensive system of plants against multiple pathogens by competing for resources, hyperparasitism or producing bioactive compounds with antimicrobial properties. There is an ever-increasing interest for obtaining new and environmentally friendly products to use in the fight against pathogens. With this purpose, Byssochlamys spectabilis (anamorph Paecilomyces variotii), which is a fungal species that commonly occurs, was evaluated as an antagonistic organism towards three phytopathogens (Biscogniauxia mediterranea, Fusarium moniliforme and Phytophthora cinnamomi). First, an in vitro experiment was designed to test the effect that the endophyte filtrate had on the three pathogens. The endophyte filtrate decreased the radius growth rate of F. moniliforme by nearly 10%. Consequently, the antagonism between B. spectabilis and F. moniliforme was evaluated in Lolium rigidum plants under greenhouse conditions by means of co-inoculations. The endophyte produced a decrease of 50–75% in the disease severity caused by the pathogen in the earliest infection stages. Crude extracts of B. spectabilis were obtained to determine the secondary metabolites responsible for such an effect. The bioactivity-guided chromatography and HPLC-MS (high performance liquid chromatography coupled with mass spectrometry) of the active fraction suggested that the antibiotic activity was caused by viriditoxin. In conclusion, the fungal endophyte B. spectabilis and/or its bioactive compounds showed antagonism towards several phytopathogens and deserves further study to investigate its actual potential for use as a biocontrol agent.
Impact of NK cell repertoires on immunotherapy in acute myelod leukemia

Natural killer (NK) cells are lymphocytes endowed with cytotoxicity against aberrant cells, including transformed and virus-infected cells. NK cell function is dictated by a fine-tuned interplay between activating and inhibitory receptors expressed on the NK cell surface. While the different activating receptors interact with unique ligands present on healthy or transformed cells, inhibitory NKG2A and killer immunoglobulin-like receptors (KIRs) invariably recognize HLA class I molecules. The purpose of this thesis was to elucidate how interactions between inhibitory NK cell receptors and HLA class I impact on anti-leukemic functions of NK cells and on NK cell-mediated termination of inflammation. In a phase IV trial, 81 AML patients received histamine dihydrochloride and low-dose interleukin-2 (HDC/IL-2) for the prevention of recurrence of leukemia after the completion of chemotherapy. The trial comprised immunophenotyping of serial blood samples along with KIR/HLA genotyping and assessment of cytomegalovirus (CMV) serostatus. Results from papers I and II imply a beneficial role of NK cell subsets that are less inhibited by HLA while prior CMV infection, which promotes the expression of additional KIRs, impacted negatively on relapse risk and survival. Additionally, a single nucleotide polymorphism in HLA-B that dictates NK cell inhibition to be preferentially mediated by NKG2A impacted positively on outcome in this trial (paper III). The relevance of the interplay between activating and HLA-mediated inhibitory signaling was further illustrated in a non-malignant setting in paper IV, where modulation of NK cell receptor ligands expressed by inflammatory neutrophils was associated with enhanced susceptibility to NK cell cytotoxicity. In conclusion, these studies support i) that low-grade KIR-mediated inhibition of NK cells is relevant for the benefit of relapse-preventive immunotherapy in AML and ii) that NK cells participate in the resolution of inflammation.
Sak and its potential role in the DNA damage response.

The Plk family of serine/threonine kinaese are key players in the cell cycle, centrosome regulation and DNA damage pathways. Sak's (Plk4) involvement in these processes is not fully established. We examined Sak’s role in DNA damage pathways and found that full length wild-type Sak protein was found to be subjected to phosphorylation both in the presence and absence of UV. This post-translational modification did not occur in the Sak polo-box and cryptic polo-box domains. Furthermore, we established that Sak interacts with two key DNA damage proteins, ATR and Chkl. Additionally, another DNA damage protein Chk2, which also interacts with Sak, was found to be a substrate of Sak. Interestingly, UV exposure abolished phosphorylation of Chk2 by Sak, suggesting that Sak is in fact inhibited by UV radiation. These findings suggest that Sak may play a role in the DNA damage response pathway.
Roles of the Hedgehog Signaling Pathway in Skin Development, Homeostasis and Cancer

Abstract: The epidermis is the outermost layer of skin and provides a protective barrier against 9 environmental insults. It is a rapidly renewing tissue undergoing constant regeneration, 10 maintained by several types of stem cells. Hedgehog (HH) ligands activate one of the fundamental 11 signaling pathways that contribute to epidermal development, homeostasis and repair. The HH 12 pathway interacts with other signal transduction pathways such as those activated by Wnt and 13 bone morphogenetic protein. Furthermore, aberrant activation of HH signaling is associated with 14 various tumors, including basal cell carcinoma. Therefore, an understanding of the regulatory 15 mechanisms of the HH signaling pathway is important to elucidate fundamental mechanisms 16 underlying both organogenesis and carcinogenesis. In this review, we discuss the role of the HH 17 signaling pathway in skin development, homeostasis and basal cell carcinoma formation, 18 providing an update of current knowledge in this field. 19
Cross-reactive immunity drives global oscillation and opposed alternation patterns of seasonal influenza A viruses

Several human pathogens exhibit distinct patterns of seasonality and circulate as pairs of discrete strains. For instance, the activity of the two co-circulating influenza A virus subtypes oscillates and peaks during winter seasons of the world’s temperate climate zones. These periods of increased activity are usually caused by a single dominant subtype. Alternation of dominant strains in successive influenza seasons makes epidemic forecasting a major challenge. From the start of the 2009 influenza pandemic we enrolled influenza A virus infected patients (n = 2,980) in a global prospective clinical study. Complete hemagglutinin (HA) sequences were obtained from 1,078 A/H1N1 and 1,033 A/H3N2 viruses and were linked to patient data. We then used phylodynamics to construct high resolution spatio-temporal phylogenetic HA trees and estimated global influenza A effective reproductive numbers (R) over time (2009-2013). We demonstrate that R, a parameter to define host immunity, oscillates around R = 1 with a clear opposed alternation pattern between phases of the A/H1N1 and A/H3N2 subtypes. Moreover, we find a similar alternation pattern for the number of global virus migration events between the sampled geographical locations. Both observations suggest a between-strain competition for susceptible hosts on a global level. Extrinsic factors that affect person-to-person transmission are a major driver of influenza seasonality, which forces influenza epidemics to coincide with winter seasons. The data presented here indicate that also cross-reactive host immunity is a key intrinsic driver of global influenza seasonality, which determines the outcome of competition between influenza A virus strains at the onset of each epidemic season. Significance statement Annual influenza epidemics coincide with winter seasons in many parts of the world. Environmental factors, such as air humidity variation or temperature change, are commonly believed to drive these seasonality patterns. Interestingly, three out of the four latest pandemics (1918, 1968 and 2009) did not spread in winter initially, but during summer. This questions to what extent other factors could also impact virus spread among humans. We demonstrate that cross-reactive host immunity is a key factor. It drives the well-known seasonal patterns of virus activity oscillation and alternation of the dominant influenza virus subtype in successive seasons. Furthermore, this factor may also explain the efficient spread of pandemic viruses during summer when cross-reactive host immunity is relatively low.
Assessment of the genetic determinants involved in the expression of hight level of oxacilin resistence in contemporany clinical methicillin-resistant Staphylococcus aureus (MRSA) strains

iv Resumo . v Table of contents . vi Figures Index . ix Tables Index . x Abbreviations . xi Chapter I Introduction. 1 1. Staphylococcus aureus – General Features . 1 1.1. S. aureus cell wall . 1 1.2. Colonization and infection . 2 1.3. S. aureus genome . 2 2. Beta-lactam (β-lactam) resistance in S. aureus . 3 2.1. Mechanism of action of β-lactam antibiotics . 4 2.2. β – lactam resistance in S. aureus . 4 2.2.1. Penicillin resistance . 4 2.2.2. Methicillin resistance . 5 3. Staphylococcal cassette chromosome mec SCCmec . 6 3.1. Integration and excision of SCCmec elements . 9 3.2. Origin and evolution of the SCCmec . 10 3.3. MRSA clones . 10 4. Heterogeneous β-lactam resistance . 13 5. Whole genome sequencing (WGS) . 13 6. Aim.15 Chapter II – Materials and Methods . 16
Immune responses to conserved influenza epitopes : lessons for peptide vaccination strategies

Seasonal influenza epidemics lead to severe flu in 3 to 5 million individuals and emerging pandemic influenza strains pose an even greater threat to society. We describe a clinical trial in which vaccine-specific responses were measured during two consecutive influenza seasons, including the season in which the 2009 pandemic virus emerged, and showed that these vaccines induced both humoral and cellular responses. However, these responses are unlikely to be protective against newly emerging strains, due to the variable nature of influenza virus. Therefore, the other chapters in this thesis describe concepts within peptide-based vaccination strategies, which is one method to induce responses to highly conserved sequences of influenza virus. We evaluated a concept based on long peptides directed to highly conserved B and T cell epitopes and showed that this vaccine was capable of inducing both humoral and cellular immune responses. Furthermore, the vaccine provided partial protection against infection in an animal model. We also described another successful strategy to enhance the immunogenicity of minimal peptides by modification of these peptides and proceeded with formulations to improve delivery of these minimal peptides. Altogether, the findings in this thesis may contribute to the development of the next generation influenza vaccines.
Inhibitory Effects of BVAN08 on the Growth of Experimental Tumor Cell Lines both In Vivo and In Vitro

In order to study the mechanism of a novel vanillin derivative BVAN08, provide evidence and experimental data for developing it as a new potential anticancer drug. Hepatic cancer HepG2 cells and normal LO2 cells were used to investigate cytotoxicity of BVAN08. The MTT and colony-forming ability assays showed that BVAN08 significantly sensitized HepG2 cells to radiation rather than LO2 cells. Moreover, BVAN08 inhibited the growth of HepG2 cells in nude mice and exerted no effects on body weight and the number of the peripheral white blood cells. The immunohistochemistry results indicated that the DNA-PKcs expression the BVAN08 group tumor was lower than that of control group. BVAN08 obviously inhibits proliferation of HepG2 cells in vitro and in vivo supporting it as a promising anticancer drug candidate.
The evaluation of biological activity of methanolic extracts of Solanum nigrum and molecular docking analysis of selected phytoconstituents against vimentin

Background: Solanum nigrum L. (SN), commonly known as black nightshade or Makoi in India, is well documented in Ayurveda, the indigenous system of medicine, for its medicinal properties. However, it has still not garnered considerable attention for modern therapeutic use. In the present study, in vitro activities of methanolic extract(s) of dried roots, stems and leaves of S. nigrum were evaluated against human cancer cell lines MDA, Hep G2, A549 and normal cell line Vero. Methods: The percentage viability of the cell lines was determined using MTT assay. Antibacterial activity of the extracts was tested against S. aureus and E. coli using disc diffusion method. Molecular docking studies were carried out to assess the inhibitory action of selected phytoconstituents belonging to the class of steroidal glycoalkaloids (SGAs) and steroidal saponins (SSs) against cytoskeletal proteins viz. actin (G- and F-), tubulin (alpha and beta) and vimentin. Results: HepG2 cells were found to be most susceptible to SN extracts. Leaf extract of SN showed significant anticancer activity against Hep G2 and MDA cells (IC50 values approx. 20 µg/ml). AGE of isolated DNA from treated cancer cells revealed characteristic ladder like fragmentation, a hallmark of apoptosis. HPLC profiling demonstrated the presence of alpha-solanine in all extracts. Molecular docking analysis revealed that SGAs displayed potent binding to the intermediate filament protein vimentin (Ki 1.0-8.1 µM) whereas the SSs displayed moderate to low binding to vimentin. Conclusion: SN methanolic extracts inhibited proliferation and induced apoptosis in human cancer cell lines and thus, warrant further investigation.
Differential effects of plant growth regulators on physiology, steviol glycosides content, and antioxidant capacity in micropropagated tissues of Stevia rebaudiana

Abstract Plants naturally produce secondary metabolites on exposure to abiotic/biotic stress. Production of secondary metabolites, like phenols or flavonoids, is a defence mechanism against different stresses. This study explores the influence of plant growth regulators (PGRs) on the growth and secondary metabolites of in vitro grown tissues of zero calorie sweetener, Stevia rebaudiana. An efficient regeneration of this valuable plant under the influence of PGRs was conducted, and quantification of physiology parameters, steviol glycosides (SGs) and various antioxidant activities in callus, shoots and regenerated plants was performed. Significantly highest explant response was achieved by 2 mg/L of 6-benzyl aminopurine (BAP) and 0.5 mg/L of 2,4-dichlorophenoxy acetic acid (2,4-D) combination in case of callogenesis, while shoot and root organogenesis was best illustrated by control and 0.5 mg/L of indole acetic acid (IAA) treatment, respectively. Regarding SGs formation in leaves, significantly greater content (2.07% and 0.93%) was obtained by control in case of rebaudioside A (Reb A) and 2 mg/L of BAP in case of stevioside (ST). Leaves of rooted-shoots produced significantly highest Reb A (4.21%) and ST (2.22%) content in case of 1 mg/L of IAA and 0.25 mg/L of IAA inoculation in Murashige and Skoog growth medium, respectively. Similarly, differential effects of PGRs were elucidated in case of all in vitro grown tissues on antioxidant properties. The study concludes that secondary metabolites can be efficiently produced in in vitro culture so can be employed in bioreactors.
Witches' Broom Disease of Small-Fruited Acid Lime Trees in Oman: First MLO Disease of Citrus

Lime trees are grown on a large scale in the Sultanate of Oman along the coast of the Gulf of Oman in the northern part. In the areas of El-Morer, Shinas and Liwa, many lime trees are affected by a disease which practically kills the trees within a few years and several growers have had to pull out whole orchards. The symptoms of the disease start with the appearance of a witches' broom (WB) and soon, within 3-4 yr, the tree is covered with many WBs. WBs are very conspicuous and characterized by their very small, pale-green leaves, which eventually dry up. Fruit production ceases. Electron microscopy revealed the presence of numerous mycoplasma-! ike organisms (MLO) in the sieve tubes of WB leaves. The MLOs completely fill some of the sieve tubes. The disease appeared some 10 yr ago, but its origin is unknown. Growers became aware of it about 5 yr ago, and now the situation is truly alarming. The disease seems to be spreading along the Coast from North to South. Since MLOs are involved, leafhoppers or psyllas are potential insect-vectors. Lime is the only citrus grown in the affected area, and nothing is known as yet about the susceptibility of other citrus species. WB disease is associated with a nonhelical, mycoplasma-like organism which has not yet been culture. WB is the first disease of citrus associated with MLOs. Index words. mycoplasma-like organism, Oman, Mexican lime. This report is the result of a survey in the Sultanate of Oman from April 5 to 13, 1986 to study a so-called "witches' broom disease" affecting small-fruited acid limes. The disease is restricted so far to the Northern part of the country along the coastal plain (North Batina) and extends from the border with the United Arab Emirates to Khaboura which appears to be the southernmost limit of the affected region.
Cétuximab dans le traitement du cancer colorectal métastatique réfractaire à l'irinotécan: évaluation de facteurs cliniques prédictifs de réponse

Objectif : L'objectif etait d'identifier des facteurs cliniques predictifs de reponse au cetuximab-irinotecan (CI) chez des patients presentant un cancer colorectal metastatique refractaire a l'irinotecan. Patients et methodes : Analyse retrospective de patients traites par cetuximab (400mg/m2 semaine 1 puis 250mg/m2 les semaines suivantes) plus irinotecan (180mg/m2/2semaines). Les donnees cliniques suivantes ont ete evaluees en analyse uni-variees et multi-variees : donnees demographiques, duree de la maladie, reponse aux chimiotherapies anterieures, intervalle libre sans irinotecan, nombre de sites metastatiques et statut EGFR tumoral par immunohistochimie. Resultats : 311 patients ont ete analyses. Le taux de reponse objective sous CI etait de 26%. En analyse univariee, une reponse anterieure a l'irinotecan, une duree d'evolution >= 24 mois, une evolution metastatique >= 18mois, un intervalle libre sans irinotecan >=1,8mois et la presence d'un seul site metastatique etaient predictifs de reponse au CI. En analyse multivariee, une valeur predictive independante etait confirmee pour la reponse anterieure a l'irinotecan, duree d'evolution de la maladie et le nombre de sites metastatiques. Le statut EGFR n'avait pas de valeur predictive. Sur 35 patients EGFR negatifs, chez 14(40%) une reponse objective a ete constatee. Conclusion : La reponse anterieure a l'irinotecan, la duree d'evolution de la maladie et le nombre de sites metastatiques sont des facteurs predictifs independants de reponse au cetuximab. Cette etude apporte de nouvelles preuves de l'interet de traiter aussi les patients EGFR negatifs par cetuximab.
Regulatory redox state in tree seeds

Peroxiredoxins (Prx) are important regulators of the redox status of tree seeds during maturation and long-term storage. Thioredoxins (Trx) are redox transmitters and thereby regulate Prx activity. Current research is focused on the association of Trx with Prx in tree seeds differing in the tolerance to desiccation. The results will allow for better understanding the regulation of the redox status in orthodox, recalcitrant, and intermediate seeds. The findings will also elucidate the role of the redox status during the loss of viability of sensitive seeds during drying and long-term storage.
EFFECTS OF SUPPLEMENTAL NEEM (Azadirachta indica) AND GARLIC (Allium sativum) ON GROWTH AND CARCASS YIELD OF FINISHING BROILER

This study was conducted to investigate the effects of feeding diets containing Neem Leaf Meal (NLM), Garlic Meal (GM) and their combinations (NLM + GM) on growth performance and carcass yield of finishing broiler. A total of 180 day-old Cobb broiler chickens were divided into twelve groups of fifteen chicks with three replicate of five chicks each. The diet contained NLM, GM and NLM + GM at four levels of inclusion (0mg/kg, 500mg/kg, 1000mg/kg and 1500mg/kg). The experiment was arranged in a 3 × 4 factorial layout in a completely randomized design. Additives and levels of inclusion had no significant (P>0.05) influence on performance parameters except feed intake which was influenced (p 0.05) influence on performance parameters except feed intake which was influenced (p<0.05) by NLM + GM and 1000mg/kg levels of inclusion. Final live weight (2516.67g/bird), weight gain (1742.00g/bird), daily weight gain (62.2g/bird/day) and feed conversion ratio (2.32) were improved (p<0.05) at 1500mg/kg levels of inclusion of NLM + GM. Thigh (11.68%), wings (8.44), neck (4.23%) and gizzard (2.13%) of birds fed GM were improved (P<0.05) than those of NLM. Carcass weight was influenced (p<0.05) by additives at various inclusion levels with wings (9.01%), head (3.39%), neck (4.52%), shanks (4.49%) and gizzard (2.42%) highest (p<0.05) in birds fed GM at 1500mg/kg levels of inclusion than those of 0mg/kg levels of inclusion. It was concluded that the use of NLM + GM as additives yielded commendable result on performance and carcass weight of finishing broiler birds Keywords : Neem, garlic, broilers, performance, carcass characteristics.
Bioprocessing of wheat (Triticum aestivum cv. Kronstad) bran from Northwest Mexico: effects on ferulic acid bioaccessibility in breads

ABSTRACT Evaluating the biological potential of wheat grain cultivated in northwestern Mexico is important because it mainly varies according to the cultivar and production area. The aim of the present study was to evaluate ferulic acid (FA) bioaccessibility in breads supplemented with bioprocessed bran. Bran that was bioprocessed with xylanase enzyme (EB), yeast fermentation (FB), and a combination of both treatments (FEB) showed a higher total phenol content and antioxidant capacity compared with native bran (NB), and the majority of these components were found in a bound fraction. For NB and bioprocessed bran, FA was found at higher levels compared to the other hydroxycinnamic acids evaluated. Bioprocessing increased the free FA content six-fold compared to NB. The % bioaccessibility of FA in different breads increased in the following order: FEB<NB<FB<EB. The addition of bioprocessed bran is may be the simple way to increase the amount of bioactive compounds in a bread product.