Miracle-dz/UniFAR-FTUs huggingface dataset:
Population structure and siderophore production in commensal Escherichia coli

Abstract The factors involved in the diversity, transition and persistence of commensal Escherichia coli, both between and within hosts, are not fully understood. The aim of this project was to develop and use comparative approaches to investigate traits associated with colonisation of the gut by taking advantage of two collections of natural isolates of E. coli, the ECOR (host-associated) and GMB (plant-associated) collections. A new method for uniquely tagging and monitoring individual E. coli strains was developed to facilitate the assessment of large numbers of strains in complex environments, such as the gut. Competition studies between ‘barcoded’ strains show that this technique has a high sensitivity enabling the identification of E. coli present in the population at low levels, which may be undetected using currently available methods. Together with genome-wide association studies, barcoding is a powerful tool for identifying adaptive traits associated with the environment. One trait linked to E. coli gut colonisation is production of the siderophore enterobactin. Comparisons of siderophore production and the distribution of siderophore loci between the GMB and ECOR collections highlighted that faecal strains produce higher levels of siderophores and possess a larger number of siderophore systems at the population level. However, while our epidemiological data indicated a role for siderophore biosynthesis in the GI-tract, we did not observe significant differences in the competitiveness of siderophore biosynthesis mutants in a mouse model. Whether this is linked to the ability of mutants to cheat and use siderophores generated by the wild-type strain or to obtain iron through other ways remains to be determined. Overall, this study provides further details on the factors determining how the environment shapes the associated E. coli populations. This knowledge is essential to assess the relationship between the environment, the associated E. coli populations and the risk they represent to human health.
Trends in Illegal Trade of Wild Birds in Amazonas State, Brazil

This study evaluates the seizure of birds in the state of Amazonas during twenty years (1992-2011), providing information on the sale of birds in a state recognized for its significant biodiversity. We compiled a total of 2,698 seizure records of illegal wildlife trade, which were drawn up and issued by the Brazilian Institute of Environment and Renewable Natural Resources - IBAMA (the Brazilian official agency for environmental license and patrol) in the state of Amazonas, during 240 months. Reports of birds seized were found in only 297 (11%) of the seizure records analyzed. The number of bird specimens ranged from 3 to 710 per year, and the taxonomic richness ranged from 1 to 24 species. Considering all seizures, there was a richness of 40 bird species, distributed in 16 families and 10 orders. Among the families analyzed, Thraupidae was the richest, with 17 species, followed by Psittacidae, with eight species. The order Passeriformes was the most represented, with 12 genera, where Sporophila was the richest, with nine species (22.5% of total species). The Saffron Finch (Sicalis flaveola – Linnaeus, 1766), Muscovy Duck (Cairina moschata - Linnaeus, 1758) and Chestnut-bellied Seed-Finch (Sporophila angolensis - Linnaeus, 1766) together accounted for more than half (56.9%) of the total birds seized for the period. Of the species recorded in this study, five (12.5%) were listed as Endangered. Our results suggest that the illegal trade of animals in Amazonas shows a pattern different from that which has been reported in other Brazilian states. Birds were little represented in the Amazon, and the main reason for their illegal trade was related to their use as food. In addition to the cultural aspects, the richness of vertebrates in the Amazon certainly influences the choice of animals used and marketed in the Amazon region.
Genetic and Phenotypic Trends of Fertility Traits in Iranian Holstein Cows

A total of 72124 fertility records was used to estimate the genetic and phenotypic trend of fertility traits in Iranian Holstein cow from 1981 to 2007. Fertility traits in this study were: days from calving to first service (DFS), number of insemination per conception (INS), days open (DO), interval between first and last insemination (IFL), calving interval (CI) and success to first insemination (SF). The overall genetic trend in fertility traits was as desired and statistically significant. Mean breeding value of SF increase by 0.00067 percent per year. The annual genetic trends for INS, DFS, IFL, CI and DO were -0.0029 number/year, -0.062 days/year, -0.041 days/year, -0.23 days/year and -0.24 days/year, respectively. Phenotypes trends for fertility traits were unfavorable except for DFS and DO. Phenotypic trends in IFL, INS and SF were as undesirable positive. Phenotypically DO and CI did not change over the time period. Phenotypically IFL has increased 1.6 days/year and DFS has decreased 1.6 days/year. The annual phenotypic trends for INS and SF were 0.04 and -0.018, respectively.
Molecular and morphological characterisation of Ulva chaugulii, U. paschima and U. ohnoi (Ulvophyceae) from the Persian Gulf, Iran

Abstract Species of Ulva are distributed worldwide in various aquatic habitats and their morphological characters change considerably in response to environmental conditions, which makes identification in this genus problematic. All Ulva species so far described from the Persian Gulf, Iran, have been identified by classical taxonomic methods. In this study, Ulva spp. collected from the Persian Gulf were identified by combined morphological and molecular methods. We sequenced the internal transcribed spacer ITS2 and the rbcL gene in 15 specimens, representing typical morphotypes of over 50 samples. Maximum likelihood, maximum parsimony and Bayesian inference (BI) phylogenetic reconstructions using ITS and rbcL revealed clades, which we identified as Ulva chaugulii, U. paschima and U. ohnoi. These three species have not been recorded from the Persian Gulf, Iran before. The morphology of U. chaugulii differed considerably from its species description, showing further evidence for extreme intraspecific variation in morphology in this cosmopolitan genus.
Effect of Bracket’s Slot Size on Canine Position and Space Closure Rate (A Typodont Study)

Aims: This study aimed to determine the effect of newly introduced 0.020” slot size brackets on dimensional positions and space closure ratio of mandibular canine. Material and Methods: The study includes six groups according to slot sizes (0.018”, 0.020” and 0.022”) and materials of canine retraction (elastomeric power chain and closed coil spring). A 200 gm of retraction force was used on 0.017” X 0.025” stainless steel wire ligated to brackets by elastomeric ligatures along 13 mm available space. After immersion of the typodont in water bath with (50-55) C for 5 minutes, the rate of space closure were measured in millimeter using vernier (from the distal wings of canine bracket and the mesial wings of the second premolar), In both vertical and horizontal directions, digital images were taken by camera and the angle between canine extension bar )C B) and bite plane extension bar (BPB) was measured by protractor to determine tipping and rotation. Results: The results showed that 0.022” slot bracket groups had highest amount of rate of space closure tipping and rotation, while 0.020” slot brackets groups had higher space closure rate than 0.018” slot brackets groups. Conclusions: bracket slot 0.022” groups showed higher tipping, rotation and space closure rate, while 0.020” slot brackets groups had higher rate of space closure with same or better rotation and tipping control in comparison with 0.018” slot bracket groups.
Improved proliferation and osteogenic differentiation of human mesenchymal stem cells on a titanium biomaterial grafted with poly(sodium styrene sulphonate) and coated with a platelet-rich plasma proteins biofilm

In order to replace damaged or lost bone in the human body, it is necessary to produce ‘spare body parts’ which are dependent on the use of biomaterial and stem cells and are referred to as ‘tissue engineering’. Surface modification and stem cell interaction of orthopaedic implants offer a promising approach and are investigated here specifically to improve osseointegration of the biomaterial. Osseointegration of titanium implants used in orthopaedic surgery requires that osseo-progenitor cells attach and adhere to the surface, proliferate, then differentiate into osteoblasts and, finally, produce a mineralised matrix. The surface modification of titanium with anionic polymer combined with coating of platelet-rich plasma is provided to create a favourable environment to promote early and strong fixation of implants. The ability of progenitor cells to attach to the surface during early stages is important in the development of new tissue structures; therefore, we developed in our laboratory a strategy involving the grafting of titanium implants with a polymer of sodium styrene sulphonate (poly(sodium styrene sulphonate)) and a biofilm coating of platelet-rich plasma which enables human mesenchymal stem cell interactions. The resulting biomaterial, titanium-poly(sodium styrene sulphonate) and coating of platelet-rich plasma, Ti-poly(sodium styrene sulphonate)–platelet-rich plasma was developed in order to further improve the biomaterial. In this work, we studied and characterised the ‘in vitro’ response of human mesenchymal stem cells to titanium biomaterial grafted with poly(sodium styrene sulphonate) bioactive polymer and coated with platelet-rich plasma proteins (Ti-poly(sodium styrene sulphonate)–platelet-rich plasma). This study shows an increased cell proliferation with Ti-poly(sodium styrene sulphonate)–platelet-rich plasma compared to foetal calf serum and an enhancement of the Ti-poly(sodium styrene sulphonate)–platelet-rich plasma effects on osteoblast differentiation. The results suggest that Ti-poly(sodium styrene sulphonate)–platelet-rich plasma would be a suitable scaffold for bone tissue engineering.
Assessment of Bovine Raw Milk Obtained from Selected Farms in Zaria Environs Nigeria for Toxigenic Strain of Escherichia Coli

The presence of E. coli in food or water became accepted as indicative of recent faecal contamination and the possible presence of pathogens. The study therefore aims at detecting the presence of E.coli and E. coli O157 and an indication of quality assessment of the raw milk samples sold to the open market. A total of 199 composite milk samples and 13 bulk milk samples were collected from selected farms in Zaria environs and analyzed for total aerobic and coliform counts using standard cultural methods. The total bacterial and were more than 105 in 95.48% while total coliform counts was more than 100 cell/ml in 47.24% of the composite milk analysed. All the bulk samples collected had 100% bacterial and 69.2% coliform contamination. The cleaned teats had a mean of 3.03i? ½2. 13log10cfu/ml which was not significantly different (t=1.574, p=0.117) when compared to the count obtained from the teats that were unclean (3.12i? ½1.97log10cfu/ml). However, total coliform counts of composite milk samples from animals with cleaned teats had a mean of 1.42i? ½1. 05log10cfu/ml was significantly lower (t=6.418, p-0.001) than the counts of milk obtained from cows with unclean teats (2.78i? ½1.95log10cfu/ml) The incidence of Escherichia coli in the milk samples was 7.5%, when isolates were tested for enterotoxin production using the VET-RPLA kit, 14.3% of the isolates were found to possess the heat-labile toxin. All the isolates were found to be susceptible to Ceftriaxone and Ammox-Clav (n=15; %=100), one isolate was resistant to gentamycin, ciprofloxacin and chloramphenicol (n=15, 6.7%). Eight isolates were found resistant to nalixidic (n=15, 53.3%) and nine were found to be resistant to Sulphamethazole and Trimethoprim (n=15, 60%).
Long Radiative Lifetimes of Small Molecules

In this paper, we apply a theory of electronic relaxation in polyatomic molecules for the study of the anomalously long radiative lifetimes of NO2, CS2, and SO2. We have classified medium‐size molecules which exhibit intramolecular vibronic coupling into two intermediate cases, which we call the sparse intermediate case and the dense intermediate case, characterized by low and high spacing of the vibronic levels relative to the radiative width. The radiative decay in the sparse intermediate case was considered in detail, taking advantage of the coarse level spacing and the extremely short intramolecular recurrence time encountered in this case. From our model calculations, we conclude that:(a) in the sparse case, the radiative decay rate is characterized by a superposition of slowly varying exponentials;(b) the mean radiative lifetime is expressed as a radiative lifetime calculated from the integrated oscillator strength and “diluted” by the number of states within the half‐width of the manifold of couple.
Dependence of clutch predation rate of Eurasian reed warbler Acrocephalus scirpaceus on nesting site selection: A model study

Abstract The article is focused on describing a possible way of how biological data can be processed, introduces the procedures used and compares the results gained from a field ornithological study. This was carried out using statistical methods of nonparametric regression with binomial classification and probit function together with the method with forward selection, and presents the most significant outcomes. Some of the interesting findings of this study are as follows: first, a lower level of reed warbler (Acrocephalus scirpaceus Hermann 1804) nest predation by bird predators was proven in the common reed [Phragmites australis (Cavanilles) Trinius 1841] stands growing in shallow waters, compared to nests located in stands growing in deeper waters. For this field research artificial nests containing one egg made of plasticine and one egg of Japanese quail were used. Second, a negative correlation was proven between predation of nests and their distance from the nearest tree, whereas no interdependence was proven either for various nesting-site types (oligotrophic sandpits, ponds with intensive fish-pond management and ponds with extensive use) or monitoring time (during the first, resp. second nesting). Based on the methods applied, 56% of egg predation variability was clarified and last but not least, the efficiency of these statistical methods was proven for practical use in similar field research zoological studies.
Beta diversity of geometrid moths (Lepidoptera

Turnover in species composition of the extremely species-rich family Geometridae (Lep- idoptera) was investigated along an elevational gradient ranging from 1040 m to 2677 m above sea level. Moths were sampled using weak light traps (30 W) in three field periods in 1999 and 2000 in an Andean montane rainforest in the province of Zamora-Chinchipe in southern Ecuador. A total of 13 938 specimens representing 1010 species were analysed. Similarities of ensembles of all geometrid moths and of the subfamilies Ennominae and Larentiinae were calculated using the NESS index (with mmax). Ordinations performed using nonmetric multi- dimensional scaling (NMDS) and correspondence analysis depicted a gradual change of the ensem- bles along the altitudinal gradient. Extracted ordination scores significantly correlate with altitude (-0.97 0.80 and P < 0.001 in all models).
Promotive Effects of Genistein on Photosynthesis, Flavonoid Biosynthesis and Antioxidant Enzyme Activities in Ginkgo biloba

The effects of exogenous genistein (GNT) on flavonoid content and antioxidase activity in Ginkgo biloba leaves were investigated. In particular, the flavonoids, chlorophyll, anthocyanins, and soluble sugar contents, as well as the enzymes included in flavonoid biosynthesis activities and antioxidant enzymes were measured. Leaves of one-year-old ginkgo seedlings were sprayed with 0 (control), 50, 100 and 150 μmol/L GNT. Results showed that 50, 100 and 150 μmol/L GNT significantly enhanced the intercellular CO2 concentration, net photosynthetic rate, stomatal conductance, transpiration rate, and chlorophyll, soluble sugar and titratable acid contents in G. biloba. The contents of flavonoid and anthocyanins in the leaves of G. biloba treated with 50, 100 and 150 μmol/L GNT were significantly higher than of control. The results indicated that the key enzymes included in namely phenylalanine ammonia lyase, flavonoid biosynthesis, chalcone isomerase and chalcone synthase activities were markedly increased by GNT treatment. Likewise, application of GNT significantly enhanced the activities of ascorbate peroxidase, guaiacol peroxidase, catalase, and superoxide dismutase in G. biloba. These results suggest that foliar treatment with GNT may be effective measure of improving flavonoid content and beneficial antioxidant activity in the leaves of G. biloba. © 2016 Friends Science Publishers
Antitumor activity of chitosan oligosaccharides produced in ultrafiltration membrane reactor system

Chitosan oligosaccharides (COSs) were prepared and fractionated into three groups of COS [a high molecular weight COS (HMWCOS), medium molecular weight COS (LMWCOS), and low molecular weight COS (LMWCOS)] according to their molecular weight, using an ultrafiltration membrane enzymatic bioreactor designed earlier [8]. Antitumor activity of these COSs was then examined against Sarcoma 180 solid (S180) or Uterine cervix carcinoma No. 14 (Ul4) tumor cell-bearing mice. Among these COSs, MMWCOS with molecular weight range from 1.5 to 5.5 kDa effectively inhibited the growth of both tumor cells in the mice. In addition, the administration of MMWCOS resulted in increased thymus weight among lymphoid organs. The mice treated with MMWCOS showed improved survival rate and larger number of survivors after 40 days of feeding. The most effective of MMWCOS far antitumor activity in the S180- or U14-bearing mice was 20 mg/kg/day or more.
Serum enzyme activities and electrolyte concentrations of breeding donkeys (Equus asinus): effect of sex, age, lactation and/or pregnancy.

Influence of sex, age in males and lactation and/or pregnancy in females on serum activities of four enzymes and concentrations of six electrolytes in 62 apparently healthy breeding donkeys comprising of 33 males and 29 females were studied. Statistical analysis revealed that out of 10 parameters: a) Sex affected activities of four enzymes namely, ALT, AST, LDH and y-GT significantly: Females showed significantly higher values of these enzymes; b) Age in males altered only two enzymes namely LDH and y-GT while electrolytes remained unaltered. Young foals aged less than 1 year showed highest values among these parameters whereas 3-7 year and above 10 year old donkeys showed the lowest values of LDH and y-GT, respectively; c) Lactation and/or pregnancy in females affected activities of 4 enzymes ALT, ALP, LDH and y-GT and concentrations of two electrolytes i.e., K and Cl. Non-pregnant dry animals showed significantly (P<0.05) lower activities of four serum enzymes i.e., ALT, ALP, LDH and y-GT than the rest of all physiological states of females under study except AST which remained unaltered. It is concluded that physiological states, performed by corresponding hormones, leading to mild or transitional stresses play the all important regulatory role which has substantial function in the maintenance of stable homeostasis.
Selective administration of domperidone in maintenance of homeostasis in human body

Domperidone is a specific blocker of dopamine receptors. It speeds gastrointestinal peristalsis, causes prolactin release, and is used as antiemetic and tool in the study of dopaminergic mechanisms. Domperidone acts as a gastrointestinal emptying (delayed) adjunct and peristaltic stimulant. The gastroprokinetic properties of domperidone are related to its peripheral dopamine receptor blocking properties. Domperidone facilitates gastric emptying and decreases small bowel transit time by increasing esophageal and gastric peristalsis and by lowering esophageal sphincter pressure. Antiemetic: The antiemetic properties of domperidone are related to its dopamine receptor blocking activity at both the chemoreceptor trigger zone and at the gastric level. It has strong affinities for the D2 and D3 dopamine receptors, which are found in the chemoreceptor trigger zone, located just outside the blood brain barrier, which among others regulates nausea and vomiting.
Food bodies of Cecropia pachystachya (Cecropiaceae) leaves: structural and functional features suggesting complementary role to Müllerian bodies

ABSTRACT Cecropia pachystachya is a myrmecophyte which has domatia and nutritional resources used by ants of the genus Azteca. In addition to Müllerian bodies, another type of structure, food bodies (FBs), are present on the leaves of this plant, which is the focus of this study. Leaf samples were collected and prepared for light, and transmission and scanning electron microscopy. Histochemical analysis and thin layer chromatography were also employed to determine the composition of reserves. Food bodies are found in young leaves, distributed on the leaf blades and petioles. On leaf blades, FBs occur predominantly on the abaxial surface and are always associated with veins. Food bodies are emergences produced by anticlinal divisions of protodermic cells and divisions of the underlying ground tissue. Mature FBs are claviform, translucent and show fragile stalks. Similar to the epidermal cells, the inner parenchyma cells have thin walls and cytoplasm with few mitochondria and endoplasmic reticulum segments; their reserves consist of oil droplets dispersed in the cytoplasmic matrix and reducing sugars in the large central vacuole. Because of the liquid reserves that allow them to be consumed by adult ants, these FBs differ from the well-studied Müllerian bodies. Food bodies are collected by ants after stipule rupture and immediately consumed. Our results suggest that these FBs act in a complementary function to the Müllerian bodies, but this hypothesis remains to be tested. Searching for FBs, ants patrol young leaves and this seems to reduce response time to herbivory, thereby reducing leaf damage.