Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete chloroplast genome sequence of an conifer plant Torreya grandis (Pinales, Taxaceae)

Abstract Chinese Nutmeg Tree (Torreya grandis) is a species of conifer in Taxaceae, which has a wide range in eastern and south-eastern China. Torreya grandis, endemic to eastern and south-eastern China, is a large tree, which own important economic value. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of T. grandis. The genome was 136,949 bp long with 117 genes comprising of 82 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Phylogenetic analysis suggested that Torreya species formed a monophyletic clade within the Taxaceae family, and T. jackii is at the base of the tree and T. grandis and T. fargesii are sister groups of the inner clade.
Effect of Soil Type, Composting, and Antibiotic Use on Fate of Antibiotic Resistance Genes and Microbial Community Composition in Dairy and Beef Manure Applied Soils

Dairy manure is a commonly used fertilizer, but knowledge gaps remain regarding the risk and potential factors impacting the spread of antibiotic resistance genes (ARGs) from farm to fork. The objective of this study was to determine the effect of prior antibiotic use (cephapirin and pirlimycin), manure composting, and soil type on ARGs and the microbial community composition in amended soils. Microcosms representing three soil types (sandy loam, silty clay loam, and silty loam) were amended with dairy manure, with and without prior history of cephapirin and pirlimycin administration and with and without prior composting, and sacrificed with time in triplicate over 120 days. After 120-days of incubation, sul1 and tet(W) were found to be elevated in all conditions receiving manure-based amendment, regardless of prior antibiotic use history or composting. On the first day, soils receiving manure from antibiotic-treated cows contained the highest relative abundance of total ARGs based on metagenomic shotgun sequencing, but composting removed the effect of prior antibiotic use. The three soil types reacted differently to the amendments and had different levels of ARGs, with ARGs tending to persist the most in sandy loam applied soils. Application of any of the manure-based amendments changed the microbial community composition of all soils, relative to unamended controls, even after 120 days. These results indicate that soil type may be a mediating factor influencing ARG levels and while antibiotic use does impact ARGs and the microbial community, composting reduces this effect. However, the compost treated soil did not always
Country default in a monetary union

We develop a simple model of borrowing and lending within the monetary union. We characterize the default decision of the borrowing country and explore the impact that the monetary union has on the amount of borrowing, the rate of interest and the default probability. The key assumptions of the modelling strategy are that in the monetary union, the lender is risk averse with monopoly power rather than risk neutral with perfect competition. We find that the borrowing member country of the monetary union borrows more at cheaper cost vis-`a-vis a standalone borrowing country. Further, we find that forming a monetary union with high initial income disparity between the member countries leads to more and cheaper borrowing and higher default probabilities.
Applying inter-rater reliability to improve consistency in classifying PhD career outcomes

In the past year, there has been an exciting groundswell of national efforts to integrate multiple taxonomies for the transparent dissemination and analysis of PhD career outcomes. In this study, we leveraged the unique resources of the Broadening Experiences in Scientific Training Consortium to examine the reliability of the three-tiered Unified Career Outcomes Taxonomy (UCOT v.2017) that was collaboratively developed at a meeting convened by Rescuing Biomedical Research in August 2017. Using an amended version of the UCOT v.2017 (UCOT v.2017-rev1) and a new Supplementary Guidance document, we categorized over 570 PhD alumni records from three different universities. Utilizing Krippendorff’s alpha to measure the interrater reliability from nine different individuals, we determined moderate to robust reproducibility within the first two tiers of the taxonomy (Workforce Sector and Career Type); however, the reliability for the third tier (Job Function) did not meet established standards. The team identified significant sources of error, revised category definitions, improved coder training materials and processes, and tested for improved reliability through coding 219 PhD alumni records using the revised taxonomy, UCOT v.2017-rev2. Our results revealed that the changes introduced in UCOT v.2017-rev2 improved inter-rater reliability in all three tiers, and either met or exceeded the acceptable standards for reliability. A final set of clarifications were made to UCOT v.2017-rev2, resulting in UCOT v.2018 and a Finalized Guidance document. Our findings underscore the importance of carefully developing guidance documents to aid coders in the reliable and consistent categorization of alumni career outcomes. We propose periodic assessment of the UCOT v.2018 to address the natural evolution of PhD careers in the global workforce. Ultimately, we hope that UCOT v.2018 will aid in the classification and dissemination of alumni career outcomes that is essential to educating trainees, institutions, and agencies about the diversity of career options for PhDs, and therein empower all PhDs to pursue the careers of their choice.
Zinc to the sink: Genetics of increased Zn in maize kernels

Zinc (Zn) deficiency is a global health problem particularly in lowand middle-income countries where diets are cereal-based and typically lower in Zn. Biofortification, the genetic enhancement of staple foods through plant breeding is considered cost-effective and sustainable. Maize is one of the major crops grown and consumed in the regions where Zn deficiency is prevalent. But Zn concentration in maize kernels is insufficient to meet the requirements of humans. Therefore, breeding varieties with increased Zn concentration is an important goal for maize breeders. To breed Zn-biofortified varieties, it is imperative to identify germplasm with high-Zn concentration, assess their potential for grain yield and other important traits, and develop knowledge-based strategies for artificial selection. Two separate studies were conducted to assess the potential of improving maize adapted to the tropics for kernel Zn concentration. Study 1: Twenty elite inbred lines (10 quality protein maize (QPM) and 10 non-QPM) were systematically mated using a modified mating design. The generated hybrids were evaluated for kernel Zn, grain yield and flowering time in field experiments across four environments. Statistical analyses with respect to the mating design were implemented and hybrids with high-Zn and grain yield were identified. General combining ability (GCA) effects for Zn concentration were more preponderant than specific combining ability (SCA) effects, suggesting the importance of additive gene action for kernel Zn inheritance. Study 2: An association mapping panel and two bi-parental populations, evaluated for Zn concentration in three environments were used to assess the feasibility of genomic prediction for kernel Zn. Two distinct cross-validation schemes (CV1 and CV2) simulating two genomic prediction breeding scenarios were used to estimate the prediction ability (rMP) for Zn. Prediction
Cloning and expression analysis of the phytoene synthase gene in ‘Granny Smith’ apple (Malus × domestica Borkh.)

Abstract Phytoene synthase (PSY) plays a key role in the biosynthesis and accumulation of carotenoids as the first rate-limiting enzyme in the plant carotenoid pathway. In the present study, the ‘Granny Smith’ apple PSY gene, MdPSY, was cloned using in silico cloning. The length of the MdPSY was 1500 bp, which included a complete open reading frame of 1194 bp, encoding a predicted protein of 397 amino acids. Sequence analysis revealed that the ‘Granny Smith’ apple PSY protein shared high homology with MdPSY2 (99%), MdPSY1 (93.9%), FaPSY (71.8%), CuPSY (70.7%) and NtPSY (69.7%). Phylogenetic analysis showed that the MdPSY protein was closely related to the PSY protein of Rosaceae. An expression profile analysis of different tissues indicated that MdPSY expression in the roots was higher than that in other tissues. MdPSY expression was tested throughout the fruit development period. The results showed that MdPSY plays a role in carotenoid biosynthesis in ‘Granny Smith’ apple. In addition, bagging treatment inhibits PSY gene expression, which in turn affects the synthesis and accumulation of carotenoids.
The complete chloroplast genome sequence of Plantago lagopus L.

Abstract Plantago lagopus L. is the economically important medicine species plant of the family Plantaginaceae. Plantago lagopus L. is annual or perennial herbs, which is used as whole plants and seeds. Plantago lagopus L. has been used the effect of lowering blood fat, regulating blood sugar and diuresis. In this study, the complete chloroplast genome of Plantago lagopus L. was determined by the Illumina Hiseq4000 sequencing. The complete chloroplast genome of Plantago lagopus L. was 145,936 bp in length and displays a typical quadripartite structure of the large (LSC, 86,835 bp) and small (SSC, 18,431 bp) single-copy regions, separated by a pair of inverted repeat regions (IRs, 20,335 bp each). It harbours 127 functional genes, including 84 protein-coding genes, 35 transfer RNA and 8 ribosomal RNA genes species. The overall nucleotide composition was: 30.4% A, 31.3% T, 19.4% C and 18.9% G, with a total G + C content of 38.3%. Phylogenetic relationship analysis shows that Plantago lagopus L. closely related to Plantago maritima L.
The Evolution of Live Birth and the Insulin and Insulin-like Signaling Network in Sceloporus Lizards

ii Acknowledgements . iii List of Tables . v List of Figures . vi The Evolution of Viviparity in Reptiles: A Thesis Overview . 1 Chapter 1: Identifying the relationship between evolution of the insulin and insulin-like signaling network and multiple origins of viviparity in Sceloporus lizards . 13 Introduction . 14 Materials and Methods . 19 Results . 23 Discussion . 27 References . 34
Evaluation of Photomixotrophic Technique and Several Carbohydrate Sources as Affecting Banana Micropropagation

Photomixotrophic is the micropropagation technique in which living organisms use endogenous and exogenous carbohydrates as a source of energy; degree of dependence considering the sugar concentration in the medium, with presence of feeding with CO2 in addition a higher photosynthetic photon flux (PPF). Photomixotrophic enables the advertising of plantlet growth, a great survival percentage, and a descending of contamination (Nguyen et al., 2001 and Kozai, Kubota, 2005 and Nguyen et al., 2010). The CO2 enrichment can be obtained either by using a permeable gas filter(s) for vessel cap(s); which could be possessed by increasing concentration of CO2 around the cultivation vessels, or by supply of International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 10 (2018) Journal homepage: http://www.ijcmas. com
Neural underpinnnings of auditory salience natural soundscapes

Salience is the mechanism whereby attention is automatically directed towards critical stimuli. Measuring the salience of a stimulus using behavioral methods risks confounds with top-down attention, particularly in the case of natural soundscapes. A distraction paradigm is employed here to measure physiological effects of salient auditory stimuli using electroencephalography. Several such effects are presented. In particular, a stimulus entrainment response is reduced by the presentation of distractor salient sounds. A reduction in oscillatory neural responses in the gamma frequency band is also observed following salient stimuli. These measures are used to identify salient portions of the natural scene. Finally, envelope decoding methods also indicate that salient stimuli attract attention away from other, task-related sounds.
On the evolution of mutation bias in digital organisms

Mutation is one of the primary drivers of genetic change. In this work I study mutation biases, which are sets of different genetic-state inflow probabilities. Mutation biases have the potential to change the composition of genomes over time, leading to divergent short- and long-term evolutionary outcomes. I use digital organisms, self-replicating computer programs, to explore whether or not mutation biases are capable of altering the long-term adaptive behavior of populations; whether mutation biases can be competitive traits; and whether mutation biases can evolve. I find that mutation biases can alter the long-term adaptive behavior of mutation bias-obligate populations in terms of both mean fitness and complex trait evolution. I also find that mutation biases can compete against one another under a variety of conditions, meaning mutation bias can selectable over relatively-short periods of time. The competitive success of a mutation bias does not always depend upon the presence of beneficial mutations, implicating an increase in the probability of neutral mutations as a sufficient mechanism for bias selection. Finally, I demonstrate that by giving organisms a mutable mutation bias allele, populations preferentially evolve to possess specific biases over others. Overall, this work shows that mutation bias can act as a selectable trait, influencing the evolution of populations with regard to both their internal-genetic and external environments.
The complete mitochondrial genome sequence of Dendrocopos major (Aves, Piciformes, Picidae)

Abstract The great spotted woodpecker Dendrocopos major (Aves, Piciformes, Picidae) are the widespread woodpeckers from Eurasia and Northern Africa. The complete mitochondrial genome sequence consisted of 16,845 base pairs (bp) encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and 2 non-coding regions (D-loop 1, D-loop 2). The overall base composition of D. major was G + C: 47.5%, A + T: 52.5%, apparently with a slight AT bias. Phylogenetic analysis showed that D. major was closely related to Dendrocopos leucotos.
Mapping quantitative trait loci for cold tolerance in rice at seedling stage

Rice plants are sensitive to cold stress at various growth stages starting from germination to maturity. Exploitation of cold tolerance for the development of cold tolerant varieties may help in saving crop loss or cost of production in the cold prone environment. Introgression of quantitative trait loci (QTLs) conferring cold tolerance in the elite variety may be the most effective and sustainable approach to address this issue. A F2:3 mapping population of a cross between a cold susceptible variety (BR1) and a cold tolerant variety (BR18) was used to map QTLs for cold tolerance at seedling stage. Three significant QTLs on chromosomes 1, 3 and 12 associated with cold tolerance were mapped between the markers intervals of RM220-RM10829, RM546-RM7 and RM27877-RM463, respectively at a threshold LOD of 4.3 through composite interval mapping. Phenotypic contributions of these QTLs were 50.7, 39 and 52.7%, respectively. Marker information of such a large effect QTL could be used in the breeding program after necessary validation to develop cold tolerant high yielding rice varieties.
Altered chromatin localization of hybrid lethality proteins in Drosophila

Understanding hybrid incompatibilities is a fundamental pursuit in evolutionary genetics. In crosses between Drosophila melanogaster females and Drosophila simulans males, the interaction of at least three genes is necessary for hybrid male lethality: Hmr mel, Lhr sim, and gfzf sim. All three hybrid incompatibility genes are chromatin associated factors. While HMR and LHR physically bind each other and function together in a single complex, the connection between either of these proteins and gfzf remains mysterious. Here, we investigate the allele specific chromatin binding patterns of gfzf. First, our cytological analyses show that there is little difference in protein localization of GFZF between the two species except at telomeric sequences. In particular, GFZF binds the telomeric retrotransposon repeat arrays, and the differential binding of GFZF at telomeres reflects the rapid changes in sequence composition at telomeres between D. melanogaster and D. simulans. Second, we investigate the patterns of GFZF and HMR co-localization and find that the two proteins do not normally co-localize in D. melanogaster. However, in inter-species hybrids, HMR shows extensive mis-localization to GFZF sites, and this altered localization requires the presence of gfzf sim. Third, we find by ChIP-Seq that over-expression of HMR and LHR within species is sufficient to cause HMR to mis-localize to GFZF binding sites, indicating that HMR has a natural low affinity for GFZF sites. Together, these studies provide the first insights into the different properties of gfzf between D. melanogaster and D. simulans as well as a molecular interaction between gfzf and Hmr in the form of altered protein localization.
The complete mitochondrial genome of the pallid seahorse Solegnathus hardwickii (Actinopterygii; Syngnathiformes; Syngnathidae) obtained using next-generation sequencing

Abstract The complete mitochondrial genome of Solegnathus hardwickii was determined to be 16,519 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial. The complete mitochondrial genomes were obtained by conventional and long PCR. Tree constructed using maximum likelihood based on protein-coding genes and ribosomal RNAs showed close relationship of S. hardwickii with Hippocampus spp.
Bioefficacy of Alstonia boonei leaf extract against cowpea beetle Callosobrochus maculatus infesting stored cowpea seeds in storage

This study was conducted to investigate the efficacy of the oils of Alstonia boonei leaf extracted with n-hexane, petroleum ether, methane and acetone as contact insecticides against the activities of Callosobrochus maculatus in stored cowpea seed. The oils were incorporated at rates 2.0 mL per 20 g of cowpea seeds. The parameters assessed include, mortality of adult insects, oviposition and adult emergence to ascertain the control of the beetle. All concentration of the extracts used evoked 100% mortality of C. maculatus after 72 h of post treatment. The development of Callosobrochus maculatus was inversely proportional to the concentration of the oil. As the ratio of Alstonia boonei leaf oil extract increased, the mortality of the beetle increased. Therefore, complete protection of seeds and complete inhibition of adult emergence in the oils extracts of Alstonia boonei leaf were effective in controlling cowpea bruchid in stored cowpea seed.
Entomocidal properties of Monodora myristica (Dunal, 1831) and Conyza sumatrensis (Retzius, 1742-1821) extracts: Studies on two dipterous insect pests Anopheles gambiae (Giles, 1902) and Culex quinquefasciatus (Say, 1823)

Anopheles gambiae (Giles, 1902) and Culex quinquefasciatus (Say, 1832) mosquitoes are the main vectors of human malaria and lymphatic filariasis, respectively. This study aims to analyze the larvicidal, pupicidal and adulticidal properties of Monodora myristica (Dunal, 1831) and Conyza sumatrensis (Retzius, 1742-1821) extracts against An. gambiae and Cx. quinquefasciatus. The experiment was conducted in the laboratory at ambient temperature of 28 °C ± 2 °C and 75% ± 5% relative humidity. The results showed that M. myristica and C. sumatrensis extracts significantly affect all stages of An. gambiae and Cx. quinquefasciatus tested. The mosquitocidal toxicity of the two plant extracts is dosage dependent. Antilarval activity of M. myristica at rate 500 mg/L and 1,000 mg/L caused 100% mortality of An. gambiae larvae while it evoked 80% and 100% mortality of Cx. quinquefasciatus larvae. The same trend of results were also obtained on the anti-pupal and adulticidal toxicity of M. myristica and C. sumatrensis extracts. As larvicides, pupicides and adulticides, the LC50s and LC90s, after 24 h varied across plant extracts and mosquito species. C. sumatrensis attained LC50 and LC90 at higher concentration than M. myristica. On An. gambiae larvae, the LC50s after 24 h, varied from 86.95 mg/L (M. myristica) to 131.73 mg/L (C. sumatrensis). Similarly, the LC90s after 24 h on An. gambiae larvae, varied from 278.39 mg/L (M. myristica) to 131.73 mg/L (C. sumatrensis). For Cx. quinquefasciatus larvae, the LC50s after 24 h , varied from 391.41 mg/L (M. myristica) to 898.20 mg/L (C. sumatrensis). The seed extract of M. myristica exerted the best pupicidal activity among the two tested extracts with LC50 and LC90 values of 140.61 mg/L and 520.35 mg/L on An. gambiae, respectively, followed by leaf of C. sumatrensis with LC50 and LC90 values of 157.59 mg/L and 781.86 mg/L on An. gambiae, respectively. More concentrations were require to achieve 50% and 90% death of Cx. quinquefasciatus pupae. On adulticidal activity, seed of M. myristica exerted LC50 and LC90 values of 122.79 mg/L and 502.99 mg/L on An. gambiae, respectively, followed by leaf of C. sumatrensis with LC50 and Received August 11, 2018 Accepted August 30, 2018 Released August 31, 2018
Implant Coating Materials to Increase Osseointegration of Dental Implant: A Systematic Review

The literature review is intended to compare the various materials that several researchers have been used in the past ten years. Library searches are carried out electronically through the PubMed and Wiley databases to identify articles relating to the terms coating/implant coating, dental implants, and osseointegration, which are first traced using Medical Subject Heading (Mesh). The 81 articles were obtained from this literature search, but only 14 articles were considered eligible for inclusion criteria. Some coating implant materials identified and used by researchers include hydroxylapatite (HA), calcium phosphate, bisphosphonates, bioactive glass, and bioactive ceramic, ti nitride, bone stimulating factor, and fluoride have advantages and disadvantages and different coating techniques for each ingredient coating. HA Coating Material is still the most commonly used material because it provides better results and clinical properties. However, many clinical trials are still needed to obtain evidence base to ensure long-term success.