Miracle-dz/UniFAR-FTUs huggingface dataset:
The Isolation and Characterization of Proteus mirabilis from Different Clinical Samples

A total of one hundred five samples were collected from hospitals of Baghdad city during the period from 10/12/2008 to 15/3/2009. These clinical samples included: urine (50) wound swabs (25), sputum (20), and ear swabs (10). These samples were collected from the Baghdad hospital/ Teaching Laboratories, and Al-Yarmook Hospital/ Teaching Laboratories. Twenty six isolates of Proteus mirabilis were characterized according to the morphology and microscopic characteristics, along with the biochemical and confirmatory APi 20 E tests. These isolates were obtained from: urine (19), wound swabs (6), ear swabs (2), and sputum (1). The twenty selected isolates were tested for resistance against ten antibiotics and only urine samples were tested for nalidixic acid and nitrofurantoin resistance. It was shown that there were differences in the antibiotic resistance of isolates. High resistance to nitrofurantoin and ampicillin were found among isolates as (100%) and (75%) respectively while the resistance of Proteus isolates to trimethoprin /sulphamethazol, were (65%). This study also showed that resistance of isolates to gentamicin, ciprofloxacin, ceftazidime, pipracillin, cefotaxime, nalidixic acid azteronam, imipenem and amikacin were (50, 40, 40, 40, 35,27, 20,15, 5)% respectively.
Biofilm Formation and Detection of icaD Gene in Staphylococcus aureus Isolated from Clinical Specimens

S. aureusis found to be a major source of community as well as hospital acquired infections. The increase in antimicrobial resistance and emergence of multidrug resistance has become a big threat worldwide. The biofilm formation ofS. aureusinfluenced the survival and persistence in both environment and host.The study was conducted with the aim to evaluatein-vitrobiofilm formation and the presence oficaDgene inS. aureusfrom clinical isolates ofS. aureus.A total of 570 wound/pus samples were processed by standard microbiological techniques. Colony morphology, Gram’s staining and biochemical tests were used for the identification ofS. aureus. Antimicrobial susceptibility test was performed by Kirby-Bauer disc diffusion technique and methicillin-resistantS. aureuswas detected by using cefoxitin antibiotics. The production of biofilm was screened by Congo Red Agar and finally, the presence oficaDgene was determined by PCR.Out of 570 samples, a total 19.3% (110/570) samples showed the growth ofS. aureus. Among which 59.1% (65/110) were multi-drug resistant. Similarly, 26.4% (29/110) isolates were methicillin-resistantS. aureus. Among MRSA isolates 93.1% (27/29) were MDR with more than 3 classes of antibiotics. Biofilm production was shown by 95.45% (105/110) and 77.3% (85/110) isolates on Congo Red Agar and presence oficaDgene respectively.In this study, the significant association was observed in phenotypic production of biofilm and the presence oficaDgene for the genotypic expression of biofilm. There were also increasing rates of MRSA and multidrug resistanceS. aureus.
The small and efficient language network of polyglots and hyper-polyglots

Acquiring a foreign language is challenging for many adults. Yet certain individuals choose to acquire sometimes dozens of languages, and often just for fun. Is there something special about the minds and brains of such polyglots? Using robust individual-level markers of language activity, measured with fMRI, we compared native language processing in polyglots versus matched controls. Polyglots (n=17, including 9 “hyper-polyglots” with proficiency in 10-55 languages) used fewer neural resources to process language: their activations were smaller in both magnitude and extent. This difference was spatially and functionally selective: the groups were similar in their activation of two other brain networks – the multiple demand network and the default mode network. We hypothesize that the activation reduction in the language network is experientially driven, such that the acquisition and use of multiple languages makes language processing generally more efficient. However, genetic and longitudinal studies will be critical to distinguish this hypothesis from the one whereby polyglots’ brains already differ at birth or early in development. This initial characterization of polyglots’ language network opens the door to future investigations of the cognitive and neural architecture of individuals who gain mastery of multiple languages, including changes in this architecture with linguistic experiences.
Biases in GWAS – the dog that did not bark

Background Genome wide association studies (GWAS) of specific diseases are central to scientific discovery. Bias from inevitably recruiting only survivors of genetic make-up and disease specific competing risk has not been comprehensively considered. Methods We identified sources of bias using directed acyclic graphs, and tested for them in the UK Biobank GWAS by making comparisons across the survival distribution, proxied by age at recruitment. Results Associations of genetic variants with some diseases depended on their effect on survival. Variants associated with common harmful diseases had weaker or reversed associations with subsequent diseases that shared causes. Conclusion Genetic studies of diseases that involve surviving other common diseases are open to selection bias that can generate systematic type 2 error. GWAS ignoring such selection bias are most suitable for monogenetic diseases. Genetic effects on age at recruitment may indicate potential bias in disease-specific GWAS and relevance to population health.
Exchange of carbonyl sulfide (COS) between wheat soil and atmosphere

The exchange of COS between wheat soil and atmosphere was investigated by using a dynamic enclosure. The investigated soil type acted as a significant sink for the trace gas COS. Atmospheric COS mixing ratios and temperature were found to be the physicochemical parameters controlling the uptake. The uptake reached maximum about 0.6×10−12 mol · g−1 · h−1 at 15–20°C under natural ambient atmospheric conditions. The measured uptake values agree well with that calculated by Guenther algorithm.
Model Order Reduction by Krylov Subspace Methods with Global Error Bounds and Automatic Choice of Parameters

The simulation and control of complex technical systems in many fields of application, like structural mechanics, electrothermics, or acoustics, requires methods for the efficient simplification of mathematical models to achieve high precision despite limited computational capabilities. Starting from existing model reduction techniques, this thesis presents new approaches for the automatic choice of the degrees of freedom, and rigorous upper bounds for the estimation of the induced error.
Comparative Study on Quality Characteristics and Variations in Fatty Acid Composition of Different Varieties of Rapeseed and Mustard (Brassica spp.)

With a view to studying the qualitative features and the variations in fatty acid composition of 6 rapeseed (B. campestris and B. napus) and mustard (B. juncea) varieties, an experiment was conducted. Among these varieties, BARI Sarisha-14 presented the value of 168.4 which was recorded the highest. Both BARI Sarisha-11 and BARI Sarisha-14 was found with the highest iodine value of 39.44; and the highest amount of acid value was recorded from BARI Sarisha-11 (1.867). Gas-liquid chromatographic (GLC) method has been used to determine the composition of essential fatty acid in the seeds of Brassica spp. (L.). From the GLC analysis, it was found that Original Research Article Hossain et al.; AJRB, 3(3): 1-7, 2018; Article no.AJRB. 45954 2 erucic acid, oleic acid, linoleic acid and lenolenic acid were the prime fatty acids in all the varieties. Erucic acid was in the range of 41.11 – 51.28%, oleic acid was the highest both in BARI Sarisha-11 and BARI Sarisha13 contained (18.69%), while BARI Sarisha-9 contained the highest amount of the unsaturated linoleic (17.75%) and linolenic (15.83%) acids. Moreover, palmitic acid, stearic acid and archidic acid were also present in small amount.
Flexible polyandry in female flies is an adaptive response to infertile males

Infertility is common in nature despite its obvious cost to individual fitness. Rising global temperatures are predicted to decrease fertility, and male sterility is frequently used in attempts to regulate pest or disease vector populations. When males are infertile, females may mate with multiple males to ensure fertilization, and changes in female mating behavior in turn could intensify selection on male fertility. Fertility assurance is a potentially wide-spread explanation for polyandry, but whether and how it actually contributes to the evolution of polyandry is not clear. Moreover, whether a drop in male fertility would lead to a genetic increase in polyandry depends on whether females respond genetically or through behavioral plasticity to male infertility. Here, we experimentally manipulate male fertility through heat-exposure in Drosophila pseudoobscura, and test female discrimination against infertile males before and after mating. Using isogenic lines, we compare the roles of behaviorally plastic versus genetically fixed polyandry. We find that heat-exposed males are less active and attractive, and that females are more likely to remate after mating with these males. Remating rate increases with reduced reproductive output, indicating that females use current sperm storage threshold to make dynamic remating decisions. After remating with fertile males, females restore normal fecundity levels. Our results suggest that male infertility could explain the evolution of adaptively flexible polyandry, but is less likely to cause an increase in genetic polyandry.
Molecular characterization of Chenopodium quinoa Willd. using inter-simple sequence repeat (ISSR) markers

Quinua (Chenopodium quinoa Willdenow) is a pseudocereal of Amaranthace family which originated from the Andes of South America. Quinoa is an interesting plant whose capacity to tolerate adverse environmental factors and exceptional nutritional qualities warrant further research in all fields of plant biology, agronomy, ecology and biotechnology. Presently, it is an underutilized crop, which has the potential become a major crop. It has increases in importance in the world due to the nutritional quality of its grains and crop adaptability to diverse climatic conditions. In Colombia, more accurately in the Department of Narino, Cauca, Cundinamarca y Boyaca currently Quinua has had a huge boost due to their agronomic potential and different benefits derived from the production, processing and marketing of its products. The objective of this research was to characterize the genetic diversity of a collection of 82 materials of with seven microsatellite markers [inter-simple sequence repeats, (ISSRs)]. The analysis by the coefficient of Nei-Li at the level of similarity of 0.65 divided the population into four groups according to the site of origin of the materials. The value of average heterozygosity was 0.38 which is considered low compared to other studies of genetic diversity in Chenopodium. Molecular Analysis of Variance (AMOVA) and Fst demonstrate the existence of genetic variability at the intraspecific level that should be used in breeding programs of the species lead to obtaining new and better materials of quinua. Key words: Genetic diversity, microsatellites, Andean cereal.
Histological alterations of selected tissues (gill, liver, kidney and stomach) in two common fish species within two eutrophic peri-urban lakes in Zimbabwe

Pollution threatens fish health in the eutrophic lakes, Chivero and Manyame, in Zimbabwe. Histopathological tissue alterations of two commonly consumed fish: catfish, Clarias gariepinus, and; tilapia, Oreochromis niloticus, from Lakes Chivero and Manyame were assessed between 2015 and 2016. Seventy-one (71) catfish and 81 tilapia were caught using gill nets, and samples of their gills, liver, kidney and stomach tissue were collected and assessed microscopically for manifestations of disease. Pathologies observed in the gills of tilapia and catfish from both lakes included lamellar fusion, hyperplasia of primary lamellar epithelium and disintegration of secondary lamellar epithelium. Liver histopathology revealed vacuolation, presence of melanomacrophage centres and inflammatory cell infiltration in catfish and vacuolation in tilapia from both lakes. There were no significant differences (Chi-squared-test, p > 0.05) in the frequency of occurrence of some histological lesions in tissues assessed for the unrelated catfish and tilapia in the two lakes. Lamellar fusion in the gills conjoined neighbouring lamellae suggests the presence of parasites. Melanomacrophage centres observed in catfish may reflect metal pollution. Observed lesions in populations from both lakes suggest exposure to similar stressors and high tolerances and adaptation to eutrophic conditions.
Tree diversity drives associational resistance to herbivory at both forest edge and interior

Abstract Tree diversity is increasingly acknowledged as an important driver of insect herbivory. However, there is still a debate about the direction of associational effects that can range from associational resistance (i.e., less damage in mixed stands than in monocultures) to the opposite, associational susceptibility. Discrepancies among published studies may be due to the overlooked effect of spatially dependent processes such as tree location within forests. We addressed this issue by measuring crown defoliation and leaf damage made by different guilds of insect herbivores on oaks growing among conspecific versus heterospecific neighbors at forest edges versus interior, in two closed sites in SW France forests. Overall, oaks were significantly less defoliated among heterospecific neighbors (i.e., associational resistance), at both forest edge and interior. At the leaf level, guild diversity and leaf miner herbivory significantly increased with tree diversity regardless of oak location within stands. Other guilds showed no clear response to tree diversity or oak location. We showed that herbivore response to tree diversity varied among insect feeding guilds but not between forest edges and interior, with inconsistent patterns between sites. Importantly, we show that oaks were more defoliated in pure oak plots than in mixed plots at both edge and forest interior and that, on average, defoliation decreased with increasing tree diversity from one to seven species. We conclude that edge conditions could be interacting with tree diversity to regulate insect defoliation, but future investigations are needed to integrate them into the management of temperate forests, notably by better understanding the role of the landscape context.
Altitudinal implications in organ size in the Andrew’s toad (Bufo andrewsi)

Phenotypic flexibility of morphological and physiological traits within species is a common phenomenon across animal taxa. Hesse’s rule predicts that the size of an organ should exhibit an increase with increasing altitude along environmental gradients due to changes in oxygen supply and energy demands. Here, we test the prediction of Hesse’s rule by investigating geographical variation in the relative size of organs (i.e., heart, lungs, liver, and kidneys) across ten populations of Bufo andrewsi along an environmental gradient. We found that the relative size of these four specific organs did not increase with altitude or latitude across all populations. We also did not find that the relative size of the organs increased with increasing altitude among six populations located at a similar latitude and longitude, which is inconsistent with Hesse’s rule. Our findings suggest that oxygen supply and energy demands do not necessarily affect variation in organ size among populations.
Response of Soybean [Glycine max (L.)Merrill] to Irrigation at Different Growth Stages

A field experiment was carried out in rainy seasons of 2009, 2010 and 2011 to study the effect of irrigation schedules on yield, water use efficiency and other traits in soybean. Seven irrigation schedules consisted of irrigations at seedling stage (15–20 days after sowing), flower initiation stage, seed filling stage (20 days after flower initiation) and four different combinations of these 3 stages. Irrigation at flower initiation + seed filling stages produced the highest seed yield (3221 kg/ha). Maximum average values for seed index (14.59 g) and harvest index (50.87%) were recorded in this treatment. This treatment also recorded maximum net returns (₹ 44028/ha) followed by irrigation at seedling + flower initiation + seed initiation stages (₹ 42046/ha) and flower initiation stage (₹ 41880/ha). Control (no irrigation) had maximum water use efficiency (84.85 kg/ha/cm) followed by irrigation at flower initiation stage (83.30 kg/ha/cm). Studies indicated that irrigation to the soybean crop at flower initiation and seed filling stages helps to obtain the optimum yield and earn maximum net returns.
ORANGE: A CRISPR/Cas9-based genome editing toolbox for epitope tagging of endogenous proteins in neurons

The correct subcellular distribution of protein complexes establishes the complex morphology of neurons and is fundamental to their functioning. Thus, determining the dynamic distribution of proteins is essential to understand neuronal processes. Fluorescence imaging, in particular super-resolution microscopy, has become invaluable to investigate subcellular protein distribution. However, these approaches suffer from the limited ability to efficiently and reliably label endogenous proteins. We developed ORANGE: an Open Resource for the Application of Neuronal Genome Editing, that mediates targeted genomic integration of fluorescent tags in neurons. This toolbox includes a knock-in library for in-depth investigation of endogenous protein distribution, and a detailed protocol explaining how knock-in can be developed for novel targets. In combination with super-resolution microscopy, ORANGE revealed the dynamic nanoscale organization of endogenous neuronal signaling molecules, synaptic scaffolding proteins, and neurotransmitter receptors. Thus, ORANGE enables quantitation of expression and distribution for virtually any protein in neurons at high resolution and will significantly further our understanding of neuronal cell biology.
The complete mitochondrial genome and phylogenetic analysis of Acanthochitona rubrolineatus (Lischke, 1873)

Abstract We describe the complete mitochondrial genome of the important Polyplacophora species, Acanthochitona rubrolineatus. The mitogenome sequence of A. rubrolineatus is 14,988 bp, and all genes show the typical gene arrangement conforming to the Mollusca consensus. The overall base composition of the genome is T 39.0%, C 12.4%, A 31.2% and G 17.4%. The cytochrome c oxidase subunit I (COI) sequence of A. rubrolineatus and other 111 species from Chitonida were used for phylogenetic analysis by Bayesian inference and maximum-likelihood methods. The results show that A. rubrolineatus, Acanthochitona achates, and Acanthochitona defilippi is sister group to three lineages, and both together as the sister group of A. rubrolineata.
Molecular characterization of introduced sugarcane genotypes in Ethiopia using inter simple sequence repeat (ISSR) molecular markers

The major thrust of sugarcane (Saccharum spp.) variety improvement programs is to increase sugar yield in addition to biomass and energy cane for biofuel production. However, due to its genetic complexity, sugarcane has received very little research interest, despite its economic importance, and molecular marker techniques are being developed only in recent times. Furthermore, until the present date few molecular studies were carried out to evaluate sugarcane germplasm in Ethiopia. Therefore, this study was conducted at Addis Ababa University, Genetic Research Laboratory to evaluate molecular genetic diversity and establish relationships among genotypes and populations of introduced sugarcane in Ethiopia using ISSR molecular markers. Genomic DNA was extracted from silica-gel-dried leaf samples of 82 sugarcane genotypes according to cetyltrimethylammonium bromide (CTAB) method. A total of 149 scorable and reproducible bands were generated using 12 ISSR primers among which 124 were polymorphic and attributed to percentage of polymorphic loci (PPL) = 83.22%, Nei’s gene diversity (h) = 0.31, and Shannon’s information index (I) = 0.45 at genotypic level. The number and percentage of polymorphic loci of the marker ranged from 7 to 16 and 70 to 90.91%, respectively. Intra-population diversity based on percentage of polymorphic loci ranged from 28.86 to 47.65% with mean of 38.35%, Nei’s gene diversity of 0.097 to 0.171 with mean of 0.137, Shannon’s information index of 0.147 to 0.255 with mean of 0.205. Partitioning the genetic variation by AMOVA further revealed that 63.56% of the total genetic variation occurred among genotypes within population and 36.4% among population. All diversity index parameters confirm that the highest diversity was obtained from those that were obtained from France and Cuba whilst the lowest was from those of Barbados and South Africa. From Jaccard’s pairwise similarity coefficient, pairwise comparison of the seven populations of sugarcane, the genetic identity values were ranged from 0.532 to 0.700 with mean of 0.616. With all clustering analysis, most of the genotypes clustered to their respective geographical origins as there was some mixture of genotypes from different origins in the different clustering groups. The level of polymorphism observed proved that the ISSR marker system was robust at amplifying markers on sugarcane. Thus, ISSR markers detected a range of diversity from investigated sugarcane genotypes with their unique identity that deserve conservation attention and improvement programs. This molecular-based genetic information can be used for establishing proper identity of the genotypes, strategic conservation of these germplasm resources, and future improvement work of the sugarcane crop through selecting the appropriate parents in their breeding programs to maximize sugar yield and maintaining genetic diversity. Key words: Ethiopia, genetic diversity, inter simple sequence repeat (ISSR), sugarcane.
Palynological characteristics of some selected species of family Cucurbitaceae (Juss.) using light and scanning electron microscopy techniques

The pollen morphology of 11 species distributed in seven genera belonging to family Cucurbitaceae has been studied using light microscopy (LM) as well as scanning electron microscopy. Pollen morphology of this family is diverse and is almost europalynous. Nearly all types of pollen belonging to different size class and shape class with a variety of exine sculpturing are found in the family. Pollen grains are usually triporate to tricolporate, prolate, oblate‐spheroidal, spheroidal, to suboblate, radially symmetrical, and isopolar. The common exine pattern is reticulate of various forms ranging from finely reticulate to coarsely reticulate with some species having echinate type of exine ornamentation, for example, Cucurbita pepo and Praecitrullus fistulosus. Most of the studied species are somewhat triangular with respect to equatorial outlook and circular to elliptic in polar outlook. The palynological characteristics of the members of the family are useful in identification of taxa at generic level mostly. Based on the present study it is not recommended to wholly solely depend upon the pollen morphology for the identification of taxa especially at specific levels because very minor differences regarding pollen characters exist among the species of the same genera.