Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Strains Isolated from Children with Urinary Tract Infections

Background: Uropathogenic Escherichia coli (UPEC) and Klebsiella pneumoniae (K. pneumoniae) are major pathogens which cause urinary tract infections (UTI) in pediatric patients. The presence of extended-spectrum -lactamases (ESBLs) in these pathogens may further exacerbate infections and hamper successful treatment. Objectives: We undertook a study to investigate the prevalence of ESBL genetic indicators among K. pneumoniae strains isolated from pediatric patients in Tehran, Iran. Moreover, genotyping of blaCTX-M-15-positive isolates was determined through repetitive extragenic palindromic sequence polymerase chain reactions (REP-PCR). Methods: A total of 76 non-duplicate K. pneumoniae isolates were collected from outpatients admitted with UTIs at the pediatric nephrology wards of two hospitals in Tehran, Iran. The antibacterial susceptibility of K. pneumoniae isolates was determined by the disk diusion method. The isolates were examined phenotypically and genotypically for ESBL production using the combined-disk method and PCR, respectively. The blaCTX-M-positive isolates were subjected to minimal inhibitory concentration (MIC) testing for ceftazidime and cefotaxime. The clonal relationships of blaCTX-M-15-positive isolates were determined through REP-PCR. Results: The highest rates of antibiotic resistance were obtained for ampicillin (92.1%), followed by ceftazidime (40.8%), cefotaxime (40.8%), and aztreonam (39.5%). However, only one isolate (1.3%) was resistant to imipenem. Among the ESBL-positive isolates, blaCTX-M(64.5%) was the most prevalent gene, followed by blaSHV (54.8%) and blaTEM (41.9%). Of 20 blaCTX-M-carrying isolates, 14 isolates showed MICs of 256 g/mL against cefotaxime. The other six isolates had MICs of 512 g/mL. However, 16 out of 20 blaCTX-M-carrying isolates exhibited MICs of 128 g/mL against ceftazidime. The other four K. pneumoniae isolates showed MICs of 256 g/mL. Of 17 blaCTX-M-15-positiveK. pneumoniae isolates, 16 distinct REP-PCR patterns (genotypes) were obtained. Conclusions: The frequency of blaCTX-Mamong K. pneumoniae isolates was at an alarming rate, indicating that more eorts should be undertaken to track and monitor the spread of K. pneumoniae that produce CTX-M lactamases.
Natural colonization of loggerhead turtle eggs by the pathogenic fungus Fusarium oxysporum

Sea turtle nests are exposed to different environmental risks that may affect their hatching success. Human exploitation, predation by wild or domestic animals, nest flooding or severe beach erosion or accession are common causes of egg mortality. However, there is very little information about the impact of microorganisms on turtle eggs. We analyzed loggerhead turtle eggs from Boavista Island (Republic of Cabo Verde) which were incubated under different environmental conditions in order to evaluate the presence and impact of fungus. We have isolated Fusarium oxysporum from dead and live eggs after three days of incubation. This fungal species is a very well known plant pathogen that attacks a great variety of species including important commercial crops. The fungus grows imbibed within the eggshell and can colonize the yolk and the embryo. It is usually spherical and can present bright yellow, blue or orange colorations. Many fungus-colonized eggs die within a short period of time. We have also found the fungus in shells of hatched eggs. Hatchlings from infected eggs may suffer several physiological problems such as bronchopneumonia. We only detected fungus in eggs that were incubated in natural substrates. Freshly laid eggs isolated directly from the female cloacae did not show fungus development. Similar results were found when those eggs were incubated in sterilized sand. Fungus spores may be common in nesting beaches and represent a potential risk for the species conservation. Any activity that favours the presence of this fungus in the nesting beaches should be avoided.
MOLECULAR DOCKING OF COMPOUNDS FROM Chaetomium Sp. AGAINST HUMAN ESTROGEN RECEPTOR ALPHA IN SEARCHING ANTI BREAST CANCER

A study on molecular docking-based virtual screening has been conducted to select virtual hit of compounds, reported its existence in fungal endophytes of Chaetomium sp. as cytotoxic agent of breast cancer. The ligands were docked into Human Estrogen Receptor alpha (HER a ) as the protein which regulates the breast cancer growth via estradiol-estrogen receptor binding intervention. The results showed that two compounds bearing xanthone and two compounds bearing benzonaphtyridinedione scaffolds were selected as virtual hit ligands for HER a leading to the conclusion that these compounds were good to be developed as anti breast cancer.
Female Sterility in an Indica-Japonica Cross of Rice

Sterility is one of the obstacles to rice breeding for introducing useful genes by wide crossing, and many studies have reported on the sterility in indica×japonica crosses of rice. However, very few reports have dealt with female sterility. Typical female sterility was found in the backcrossed progenies that were developed in the breeding program to incorporate the blast resistance of an Indonesian variety "Tjina" into a Japanese variety "Fujisaka 5". The Fl of the cross Fujisaka 5×Tjina was backcrossed with pollens of Fujisaka 5. Plants with very low spikelet fertility were found in the selfing lines following the fourth backcross. Each panicle bore a few seeds (Fig.1), although it headed at the same time as the recurrent parent Fujisaka 5 under favorable growing conditions in mid-August. Spikelets of sterile plants opened normally and had iodine-stainable and highly fertile pollen grains in anthers, as Fujisaka 5 did (Table 6). The emasculated spikelets of Fujisaka 5 bore seeds at a high rate when they were crossed with pollens of sterile plants, but the emasculated spikelets of sterile plants set no seeds even when normal pollens of Fujisaka 5 were sprinkled over their. stigmas (Table 5). Since the defect of embryo-sac development was observed in the ovules of sterile plants (Fig.2), the sterility in these materials was due to female sterility.
Effects of 6-BA, GA4+7, and IBA on Growth Resumption of Chilled Apple Roots and Shoots

Nonchilled, nursery-grown apple (Malus domestica Borkh.) trees were subjected to all combinations of root and/or shoot chilling (5°C) or nonchilling (16°) temperatures for 1500 hr. Trees then were given one of the following six plant growth regulator treatments prior to greenhouse forcing for 30 days: no plant growth regulator; 10-sec shoot dip of either 6-BA, GA4+7, or Promalin; 10-sec root dip of IBA; or IBA on root plus Promalin on shoot. Chilling either the root or shoot alone resulted in partial budbreak, while chilling the entire tree increased budbreak and dry weight of new shoots significantly. New root growth depended primarily on chilling the root. Treatment of the shoot with 6-BA, GA4+7, or Promalin increased budbreak and replaced the requirement for root chilling for this response, but did not affect new shoot dry weight or root growth. Treating the root with IBA significantly increased new root growth, budbreak, and new shoot dry weight, and replaced the requirement for root chilling for these responses. Chemical names used: N-(phenylmethyl)-1H-purin-6-amine (BA); gibberellic acid (GA4+7); 1H-indole-3-butanoic acid (IBA); mixture of BA and GA4+7 (Promalin).
Comparing Conventional, Hybrid, and Distance Learning Courses in Horticulture

In a conventional sophomore level course entitled ‘‘Organic Farming and Gardening,’’ 114 undergraduate students registered from years 2007 to 2009. Due to high demand and insufficient classroom space, this conventional curriculum was reformattedwith identical course content into both a hybrid and a fully online version in which 361 students registered from years 2010 to 2012 and 336 students from 2013 to 2015. In comparing conventional instruction with hybrid and fully online versions over a 9-year period, few significant differences were found in final grades involving 811 students. Final class grade averages of these three learning systems ranged from 85.5% to 89.6% over their first 3-year spans. Over their 6-year span, the conventional class average of 89.6% was higher compared with 88.3% for the hybrid format and 86.8% for the online format. Student evaluation surveys assessed faculty performancewith eight evaluative questions on a 1 to 5 scale from years 2012 to 2014. No significant difference existed between teaching in person vs. remotely, averaging 4.35 for the hybrid and 4.17 for the online. An additional eight questions measured educational methodology, technology, student confidence, and class satisfaction. There were no significant differences in comparing the combined averages of 4.12 for the hybrid format and 4.00 for the online version. Student responses indicated a significant preference overall for hybrid and online course formats compared with conventional methods. Registration numbers indicated an overwhelming choice for online education with an average class enrollment of 91.0 students compared with 38.0 students for conventional classes and 25.2 students for the hybrid format.
Acanthocephala of cichlids (pisces) in Lake Malawi, Africa, with a description of Acanthogyrus (Acanthosentis) malawiensis sp. n. (Quadrigyridae) from Labeo cylindricus Peters, 1852 (Cyprinidae)

Two species of acanthocephalans are reported from fishes collected during the summer of 1996 in the southeast arm of Lake Malawi (Lake Nyasa), East Africa. The common Acanthogyrus (Acanthosentis) tilapiae (Baylis, 1948) had infected 18 cichlid and 1 bagrid host species (all new host records) netted by divers wearing scuba gear around Harbor Island or caught by hook and line in deep water. The specimens of this parasite were some of the smallest ever reported for that species. Two males of a new species, Acanthogyrus (Acanthosentis) malawiensis, are described from 2 male Labeo cylindricus (Cyprinidae). This is the fifth species of this genus and subgenus described in Africa. It is distinguished from the other 4 African and 33 mostly Asian species in that the proboscis hooks of the middle circle are longer than those of the anterior circle. The new species further differs from the other African species in proboscis and hook size, posterior hook root, trunk spination, and lemniscal form. Observations on host and geographical distribution, prevalence, and developmental stages of A. (A.) tilapiae are also reported.
Understanding the Role of Chloroplast Signalling in Plant Development and Drought Tolerance

3’-phosphoadenosine 5’-phosphate (PAP) was recently proposed as a new chloroplast retrograde signal that accumulates during drought stress. PAP is a by-product of secondary sulfur assimilation, generated by SULFOTRANSFERASES (SOTs) upon transferring of the sulfate group from 3’-phosphoadenosine 5’-phosphosulfate (PAPS) to sulfate acceptor molecules. PAP is efficiently degraded by the SAL1 phosphatase into inorganic phosphate and adenosine monophosphate (AMP). Consequently, PAP levels are normally kept at very low during plant development. Constitutive over-accumulation of this retrograde signal resulted in plants with pleiotropic altered phenotypes as demonstrated by the sal1 mutant in Arabidopsis, namely improved drought tolerance, altered rosette morphology and delayed development. These multifaceted altered phenotypes of sal1 correlate well with the many transcriptional changes, which are mainly due to the inhibition of 5’3’ EXORIBONUCLEASES (XRNs) by PAP. However, the details of downstream changes that links SAL1-PAP-XRN to the many altered phenotypes of sal1 remains poorly understood. This thesis investigates the possibility of conferring drought tolerance to plants by manipulating the SAL1 gene expression with minimal negative effects on growth, while unraveling the signalling pathway(s) contributing to sal1 altered development and drought tolerance. I hypothesised that PAP accumulation at early developmental stages is detrimental for plant growth and development while its accumulation at later stages of development or prior to drought stress is beneficiary for conferring plant drought tolerance. To test this hypothesis, two different strategies for easy manipulation of SAL1 expression were attempted: inducible silencing of SAL1 in wild-type Arabidopsis and inducible complementation of SAL1 in the sal1 mutant background. Surprisingly, efficient silencing of SAL1 could not be achieved even with a strong constitutive promoter driving the expression of SAL1-hair-pin RNA interference (hpRNAi) or SAL1-artificial microRNA (amiRNA) and inducible-silencing was similarly inefficient. On the other hand, inducible complementation of SAL1 in the sal1 mutant background allowed for better manipulation of SAL1 expression and PAP
Isolation, identification of yeast strains producing bioethanol and improvement of bioethanol production on cheese whey / Biyoetanol üreten maya türlerinin izolasyonu, tanılaması ve peynir altı suyunda biyoetanol üretiminin sağlıklaştırılması

Abstract Objective: In this study, bioethanol production on cheese whey (prehydrolysed enzymatically using β galactosidase by isolated yeast strains was investigated. Methods: The yeast strains were isolated from Algerian natural sources (soil and grape) and further were selected on the basis of high ethanol tolerance and high ethanol production on prehydrolysed cheese whey. The selected ones were identified by morphological, physiological and biochemical characteristics. Then, a molecular identification was carried out by amplification and sequencing the D1/D2 domain of 26S rDNA region. In addition, the operating parameters of fermentation such as temperature, pH and substrate concentration (mixture of glucose and galactose) were tested for efficient yeast strain. Results: Among the selected and identified yeast strains, three strain isolates were found to be able to produce bioethanol. These strains are Hanseniaspora opuntiae Z087A0VS, Candida tropicalis Z087B0VS and Candida tropicalis Z087D0VS with an identity of 99% and 100% respectively comparing with the stocked strains in data bank. Furthermore, Hanseniaspora opuntiae presents an ethanol tolerance ethanol up to 11% whereas the two other strains of Candida tolerate up to 12%. The fermentation parameters of most efficient strain were optimized, the temperature 30°C, pH 5 and sugar concentration (glucose and galactose) of 12.5% (w/v) are considered as optimum values for Candida tropicalis Z087B0VS. Conclusion: Candida tropicalis Z087B0VS can be considered as a good candidature for industrial bioethanol production.
Tunneling nanotubes (TNT)

Cell-to-cell communication coordinates the development of multicellular systems, and is mediated by soluble factors, gap junctions and the recently described tunneling nanotubes (TNT). Both TNT and gap junctions facilitate the transfer of intracellular mediators between the cytoplasm of connected cells. We recently described that HIV induced the formation of TNT in human primary macrophages in correlation with viral replication. Based on these results we hypothesized that during HIV infection, TNTs are hijacked by HIV to spread infection. TNT like structures may be a novel mechanism of amplification of HIV infection. Our findings and those of others require further investigation to identify the specific mechanims by which pathogens use TNT.
Telomeres and life histories

Developmental stressors often have long-term fitness consequences, but linking offspring traits to fitness prospects has remained a challenge. Telomere length predicts mortality in adult birds, but whether telomere dynamics also provide a link between developmental conditions and fitness prospects is not known. Here, we examine the effects of manipulated brood size on growth, telomere dynamics, and post-fledging survival in free-living jackdaws. Nestlings in enlarged broods achieved lower mass and lost 21% more telomere repeats relative to nestlings in reduced broods, showing that developmental stress accelerates telomere shortening. Adult telomere length was positively correlated with their telomere length as nestling (r = 0.83). Thus, an advantage of long telomeres in nestlings is carried through to adulthood. Nestling telomere shortening predicted post-fledging survival and recruitment independent of manipulation and fledgling mass. This effect was strong, with a three-fold difference in recruitment probability over the telomere shortening range. In contrast, absolute telomere length was neither affected by brood size manipulation, nor related to survival. We conclude that telomere loss, but not absolute telomere length, links developmental conditions to subsequent survival, and suggest that telomere shortening may provide a key to unravelling the physiological causes of developmental effects on fitness. NESTLING TELOMERE SHORTENING PREDICTS SURVIVAL 51 3 JBoonekamp-diss 04-03-2014 17:10 Pagina 51
Conservation Value, History and Legal Status of Non-Native White-Tailed Deer (Odocoileus Virginianus) on the Caribbean Island of St. Kitts

White-tailed deer (Odocoileus virginianus) have been introduced from North America to a variety of habitats throughout the world, including the Caribbean island of St. Kitts. Often, non-native species are considered detrimental to the environment; however, the social acceptance of non-native species appears to be resulting in a shift of the perceived conservation value of non-native animals, to the extent that they are sometimes viewed as normal or desirable in natural systems. White-tailed deer were protected by the government of St. Kitts and Nevis in 1987 but difficulties in administering and enforcing the laws have hampered conservation and research efforts. Recent progress in funding the implementation and enforcement of conservation laws provides an opportunity to explore the socio-political value of conserving the population of white-tailed deer before threats to their persistence cause their extirpation.
Iron Nutrition, Oxidative Stress, and Pathogen Defense

Adaptation is a challenge that plants have to undergo in order to survive in difficult environments. Nutrient deficiency, stress, and microorganism attack are abiotic and biotic factors that frequently impair plant wellness, which is reflected by low crop yield and quality. Poor crops in turn affect human nutrition. To solve these problems, it is necessary to understand the molecular and physiological mechanisms of nutrient uptake and adaptation to stress. With this knowledge, we may have the possibility to generate new plants, which offer better yield due to their better health. This chapter summarizes and compares iron uptake and assimilation as well as pathogen respons‐ es in plants and humans. We also discuss novel approaches for improving crops in the context of human food quality. iron is chelated with phytates. Photosynthesis, the electron transport chain and synthesis of chloro‐ or passing the lipid bilayer. Fe 3+ from plant sources is first re‐ duced by DCYTB. Ascorbic acid enhanced the reduction of iron in the lumen when taken together with meals. Diva‐ lent metal transporters such as DMT1 or NRAMP2 take up the reduced Fe into the cells. Fe is stored in form of ferritin or FPN further transports it into the blood plasma. There, Fe 2+ is oxidized back to Fe 3+ , which is either taken up by DMT1 transporter from macrophages or trapped by Tf for the circulation with the plasma. Cells with iron necessity the loaded Tf (holotransferrin) with the TfR, which is internalized via endocytosis. Acidification of the vesicles the release of Fe, ferritin and the empty TfR is recycled back to the plasma Iron sufficiency in the cells promotes the complexation of HFE with TfR1 and blocks further binding of holotransferrin. HFE translocate TfR2 and starts the signal cascade for the production of hepcidin. Hepcidin inhibits the transcrip‐ tion of DMT1 and triggers its internalization and degradation. On the macrophages, hepcidin causes the internaliza‐ tion and degradation of FPN as well.
Influence of spices : Murraya koenigii and Brassica juncea on rats fed atherogenic diet

Murraya koenigii leaf and Brassica juncea seeds at 10% levels were incorporated into a high fat cholesterol diet and fed to rats for 3 months. The results showed pronounced hypolipidemic effect. The plasma lipoprotein profile showed that these spices reduced remarkably the levels of cholesterol, triglycerides, phospholipids, low density lipoproteins and very low density lipoprotein fractions.
Therapeutic properties of Pleurotus species (oyster mushrooms) for atherosclerosis: A review

ABSTRACT Atherosclerosis is an impairment of the artery walls made up of two membrane layers, intima and media. Oxidative stress, hypertension, and hypercholesterolemia are the three main factors that cause atherosclerosis. These conditions are frequently found together and may cause atherogenesis to rapidly occur. The edible genus Pleurotus is commonly known as oyster mushrooms. Pleurotus spp. has been proven to have valuable medicinal attributes. Hence, they have been listed among “mushroom nutriceuticals” and categorized as both functional foods and medicinal mushrooms. In this review, we report the benefits of Pleurotus spp. for the prevention and treatment of atherosclerosis via reduction of oxidative stress, hypertension, and hypercholesterolemia in terms of the therapeutic compounds responsible. This review revealed that at least ten different types of Pleurotus spp. have been reported to have anti-atherogenic capabilities, with six of them possessing high levels of anti-atherogenic compounds such as ACE inhibitor peptide, ergothioneine, chrysin, and lovastatin. Hence, it has been demonstrated that Pleurotus spp. has great potential for use as food or extracts from fruiting bodies or mycelium in an alternative therapy for atherosclerosis, through prevention and treatment of oxidative stress, hypertension, and hypercholesterolemia.
Active Module Discovery: Integrated Approaches of Gene Co-Expression and PPI Networks and MicroRNA Data

Integrating protein-protein interaction (PPI) networks with gene expression data to extract active modules is shown to be promising in detecting meaningful biomarkers for cancer and other diseases. However, current algorithms suffer from many drawbacks such as focusing only on the highly differentially expressed genes, analyzing dependencies between genes in the PPI network only; totally neglecting the genes whose interactions are not known yet, and finally using mRNA gene expression data; ignoring other types of data such as gene mutation information and microRNAs expressions. In addition, lately, using the next generation sequencing technology to sequence the mRNA (RNA-Seq) has become the new standard for gene expression. However, existing algorithms either cannot handle the RNA-Seq data, or they return large modules which are hard to analyze. Therefore, we need new approaches to address the current drawbacks while utilizing and integrating the RNA-Seq data to the module discovery process. This work explores some of the drawbacks of current active module discovery algorithms. We first discuss the differences between RNA-Seq data and microarray data. With experimental evidence, we show that RNA-Seq is more powerful than microarray in providing better active modules at the expense of generating larger ones. Therefore, new approaches are needed to handle RNA-Seq data.