Miracle-dz/UniFAR-FTUs huggingface dataset:
An investigation of in vitro-assembled chromatin as a novel vehicle for gene delivery

A fundamental problem in non-viral gene delivery is the poor efficiency of DNA transfer into the nucleus. In the work described in this thesis, in vitro-assembled chromatin was investigated for the first time as a potential vehicle for non-viral gene delivery. Chromatin is formed by a hierarchical process of sequential folding and compaction of DNA, beginning with the formation of the basic repeating unit, the nucleosome, comprised of two turns of DNA around an octameric association of the core histones. It was reasoned that chromatin-induced compaction might facilitate the nuclear entry of large plasmids (greater than 5 kb) and provide resistance to cytoplasmic degradation. In addition, histones have intrinsic nuclear localisation sequences (NLSs) that mediate their passage to the nucleus and may provide a means for the nuclear import of the in vitro-assembled chromatin constructs as well. Since chromatin is the physiological form in which DNA occurs in the nucleus, endogenous mechanisms for the decompaction of chromatin exist, which might also facilitate decompaction and expression of the chromatinised plasmid. Histone octamers were reconstituted from recombinant Xenopus laevis core histones H2A, H2B, H3 and H4 and assembled in vitro with the reporter plasmid, pGeneGrip-RFP, into chromatin. A range of constructs was generated with stoichiometries between O and 40 octamers per plasmid. Chromatin formation was verified using sedimentation velocity ultracentrifugation, DNA supercoiling, micrococcal nuclease digestion and atomic force microscopy. Chromatinised constructs were transfected into Cos-7 and HTC cells usmg electroporation and lipofection and reporter gene expression was quantitated by flow cytometry. Unexpectedly, reporter gene expression decreased upon plasmid chromatinisation at high nucleosome densities. pGeneGrip-RFP was labelled using a fluorescein-conjugated peptide nucleic acid (PNA) hybridisatio~ probe in order to analyse gene expression and tracking in the same experiment. Flow cytometric analysis of isolated nuclei revealed that chromatinisation at high nucleosome densities corresponded to diminished nuclear accumulation of the plasmid. Greater proportions of nuclei accumulated plasmid chromatinised at high histone octamer stoichiome_tries than proportions of cells that expressed the reporter gene. This suggested that, in addition to reduced nuclear accumulation, gene expression may have been further compromised with chromatinisation at high nucleosome densities. A high affinity interaction between histones and nuclear import proteins, mediated predominantly by importin ~' was demonstrated using a modified ELISA method. Importin binding affinity was abolished when histones were assembled with DNA into chromatin, implying that nuclear import of the chromatin constructs was unlikely to be mediated via this pathway.
Analysis of Haricot Bean Market Chain: The Case of Meta District, Eastern Hararge Zone of Oromia National Regional State, Ethiopia

Production and marketing of haricot bean is constrained by different factors. Furthermore, the marketing chain, market competition, market structure, conduct and performance of haricot bean and their characteristics were not well identified in the study area. Hence, the overall objective of the study was to analyze the market system and factors affecting the supply of haricot bean in the study area. A total of 150 sample households and 36 traders were selected using simple random sampling method for interview. To identify factors affecting market supply Heckman’s two-stage model was used. The result revealed that only 14% of producers have the power to set haricot bean price and 22.67% of price was set by market, while above the average 63.33% of price was set by traders. There were six identified haricot bean market channels. Wholesalers and rural assemblers take the largest share, purchasing 52.23% and 29.41% of producer’s production, respectively. Wholesalers obtained the highest profit, which accounts for 1.70 Birr per kilogram. From a total of sampled producers, about 43% of haricot bean producers were found to be non-sellers of haricot bean due to different reasons. The four-firm Concentration Ratio implies that haricot bean market was characterized by an oligopolistic market. Variables like size of output, extension contact, improved seed and number of oxen have a positive effect on households’ decision to sale haricot bean; while family size and non-farm income determined volume of sale negatively. The coefficient of lambda was significant, indicating that the influence of unobservable factors in the producers’ decisions to participate was significant. As identified, producers were not beneficial from the production of haricot bean. Therefore, government attention is needed in improving the efficiency in production and marketing chain through strengthening institutions like cooperatives. The finding suggested that, improved seed and effective market information service have to be established to provide accurate and timely market information to producers.
Recent Developments in Hydrogen Technology , Volume. I

These volumes present the latest information on hydrogen systems with special emphasis on the economics of hydrogen, thermochemical production processes, and the use of hydrogen as a fuel for automotive and aircraft applications. Volume I explores the role of hydrogen isotopes in fusion energy. All aspects of tritium handling and processing are covered including isotope separation storage, extraction from a breeding blanket, scavenging systems, and recovery from water.
Zn(II)-Mediated Gold Nanosensors for Protein Phosphatase Assay

Protein phosphatases (PPs) have served as key molecules in a myriad of biological events. Since gold nanoparticle (AuNP)-based colorimetric assays have been preferred for enzyme activity assay, a few of attempts have been designed for the simple and rapid detection of PP activity. Here we report a simple AuNP colorimetric assay of PP activity using hexahistidine-tagged phosphopeptides and divalent metal ions, which does not require antibody and rare chemical. Among metal ions including nickel (II), copper(II), cobalt(II), magnesium (II), manganese (II), and zinc(II), only zinc (II) triggered self-assembly of AuNPs in the presence of hexahistidine-tagged phosphopeptides. In contrast, PP1 caused dephosphorylation of peptides, leading to no change in the color of the AuNP solution. As a result, the PP activity was easily quantified by the extinction ratio (E520/E700) of the colloidal gold assembly, where there was a linear correlation between the PP concentration and the extinction ratio. Most importantly, this method was successfully used for analyzing protein phosphatase 2A (PP2A) activity in immunoprecipitated plant extracts. Based on the results, we anticipate that out method will find the applications to monitor the activities of various PPs and their inhibition in a rapid format.
Unraveling the complexity of Corbicula clams invasion in Lake Garda (Italy)

Lake Garda, the largest Italian lake, is suffering from the introduction of several non-indigenous species during the last decades and can now be considered one of the main European freshwater hotspots of xenodiversity. Among the Bivalvia (Veneroidea, Cyrenidae), Corbicula fluminea and Corbicula fluminalis were first recorded in 2002 and 2008 respectively, and are now widespread in the southern part of the basin. Recent observation of specimens that did not resemble either of these taxa, suggested that the populations of invasive Corbicula of Lake Garda could include some other taxa not previously recorded. With this aim, a thoroughly characterization of Corbicula shells found at Lake Garda was made. By studying morphometric parameters and comparing them with specimens collected in Spain (Ebro and Ter rivers), the presence in Lake Garda of two other related species not previously recorded in Italy, namely C. leana and C. largillierti, has been confirmed. The syntopic presence of at least four species of this genus in a single environment is a singular occurrence both in Italy and Europe.
A Comparative HPLC Analysis of Myricetin, Quercetin and Kaempferol Flavonoids Isolated From Gambian and Indian Moringa oleifera Leaves

Moringa oleifera has been used for centuries as a traditional medicine in a number of sub-tropical countries. Recent studies have found it to be rich in flavonoids that exhibit antioxidant activity both in vitro and in vivo. In this study slightly modified conditions were examined in order to maximise the yield of these compounds in particular; Myricetin, Quercetin and Kaempferol. Quantitative analysis of these flavonoids were established using reverse phase ion-pairing High Performance Liquid Chromatography (HPLC) at a wavelength of 370 nm. The method development was carried out following the International Conference for Harmonization guidelines. It was found that refluxing with 0.10 M hydrochloric acid for 24 hour provided high yields of the flavonols (myricetin 292 mg/kg, quercetin 1099 mg/kg and kaempferol 133 mg/kg). There was a significant difference in the yield of these flavonols originating from the different geographical locations, with Community Forest Management Farm (CFM Farm) yielding the highest quantity of the flavonols under the conditions applied.
Genotyping of groups of cows to improve genomic breeding values of new traits

Funding information Arbeitsgemeinschaft Süddeutscher Rinderzuchtund Besamungsorganisationen e.V. Abstract Genotyping females and including them into the reference set for genomic predictions in dairy cattle is considered to provide gains in reliabilities of estimated breeding values for selection candidates. This should especially be true for low heritability traits. By the use of simulation, we extended a genomic reference set for an existing trait by including a fixed number of genotyped first‐crop daughters for one or two generations of reference sires. Moreover, we calculated results for the effects of a similar strategy in a situation where for a new trait the recording of phenotypes has recently started. For this case, we compared the effect of two different genotyping strategies: first, to phenotype cows but to genotype their sires only, and second, to collect phenotypes and genotypes on the same cows. We studied the effects on validation reliabilities and unbiasedness of predicted values for selection candidates. We found that by extending the reference set with genotyped daughters it is possible to increase the validation reliability of genomic breeding values. In the case of a new trait, it is always better to collect and use genotypes and phenotypes on the same animals instead of using only sire genotypes. We found that the benefits that can be achieved are sensitive to the sampling strategy used when selecting females for genotyping.
Layer 5 Circuits in V1 Differentially Control Visuomotor Behavior

Sensory areas of the mammalian neocortex are thought to act as distribution hubs, transmitting information about the external environment to various cortical and subcortical structures in order to generate adaptive behavior. However, the exact role of cortical circuits in sensory perception remains unclear. Within primary visual cortex (V1), various populations of pyramidal neurons (PNs) send axonal projections to distinct targets, suggesting multiple cellular networks that may be independently engaged during the generation of behavior. Here, we investigated whether PN subpopulations differentially support sensory-guided performance by training mice in a visual detection task based on eyeblink conditioning. Applying 2-photon calcium imaging and optogenetic manipulation of anatomically-defined PNs in behaving animals, we show that layer 5 corticopontine neurons strongly encode task information and are selectively necessary for performance. These results contrast with recent observations of operant behavior showing a limited role for the neocortex in sensory detection. Instead, our findings support a model in which target-specific cortical subnetworks form the basis for adaptive behavior by directing relevant information to downstream brain areas. Overall, this work highlights the potential for neurons to form physically interspersed but functionally segregated networks capable of parallel, independent control of perception and behavior.
Cause‐specific mortality of the world’s terrestrial vertebrates

Follow this and additional works at: https://digitalcommons.unl. edu/icwdm_usdanwrc Part of the Natural Resources and Conservation Commons, Natural Resources Management and Policy Commons, Other Environmental Sciences Commons, Other Veterinary Medicine Commons, Population Biology Commons, Terrestrial and Aquatic Ecology Commons, Veterinary Infectious Diseases Commons, Veterinary Microbiology and Immunobiology Commons, Veterinary Preventive Medicine, Epidemiology, and Public Health Commons, and the Zoology Commons
Hypoglycemic, Antihyperlipidemic and Antioxidant Effects of Manniophyton fulvum Aqueous Root Extract on Streptozotocin-induced Hyperglycemic Wistar Rats

This study investigated the hypoglycemic effect of M. fulvum on streptozotocin (STZ)-induced hyperglycemia in Wistar rats. The oxidative damage in the blood, liver, pancreas and kidney cells, hepatic enzyme activities and lipid profile of the Wistar rats were also ascertained. Rats were exposed to STZ alone at 160 mg/kg body weight for one week to induced hyperglycemia before treatment with M. fulvum at 83 and 113 mg/kg for 28 consecutive days. Results showed significant elevation in the levels of blood glucose level, amylase activity, serum lipid profile and serum renal markers (total protein, urea and creatinine) in the hyperglycemic rats. Moreover, streptozotocin-Original induced hyperglycemic rats showed significantly ( p < 0.05) reduced antioxidant status (reduced levels of superoxide dismutase and catalase activities as well as decreased in reduced glutathione and increased level of malondialdehide). M. fulvum was able to demonstrate marked hypoglycemic effect and ameliorate the above mentioned biochemical markers. Streptozotocin-induced rats had significant histopathological damages found in the pancreas when compared with the control. The present study shows that M. fulvum possesses significant hypoglycemic, antihyperlipidemic and antioxidant effects in streptozotocin-induced hyperglycemic rats due to its ability to effectively reduce or ameliorate the increase in blood glucose levels, lipid profile and oxidative damages.
Wind design spectra for generalisation

Previous research has shown that wind acceleration components produce a signal that can vibrate single-degree of-freedom oscillators, whose dynamic responses enable to configure design spectra for structures subject to wind. These wind design spectra present an alternative method for evaluating the dynamic response of structures and are a suitable tool for running modal analyses. Here, a generalised method for producing wind design spectra is proposed. The method consists of scaling existing spectra to adjust to a wider range of building properties and terrain conditions. The modelling technique is tested on a benchmark building to prove that its results are consistent with experimental evidence reported in the past.
Mixture of tree species enhances stability of the soil bacterial community through phylogenetic diversity

The composition of tree species might influence microbial diversity considerably, yet investigation of the consequences of changes in diversity for stability of the microbial community is still in its early stages. Understanding how diversity governs community stability is vital for predicting the response of an ecosystem to environmental changes. Phylogenetic diversity (PD) describes the distinct evolution of species in a community, and might be useful for estimating the effects of biodiversity on ecosystem function and stability. High‐throughput 16S rRNA gene sequencing was used to examine soil bacterial phylogenetic distances, phylogenetic diversity and interactions between individuals in five single‐species plantations and three mixed‐species plantations. The plantations were established on the same initial substrate, and sampling was at 68 relatively spatially independent sites. Our results showed that mixed tree species enhanced soil bacterial phylogenetic diversity and community stability, and that phylogenetic diversity had a positive effect on stability of the soil microbial community. We also found evidence that microbial communities characterized by distantly related species with weak interactions were more stable in mixed plantations than communities with strong interactions in single‐species plantations. These results may be explained by the “insurance hypothesis”, that large phylogenetic diversity of microbial communities, which share different ecological niches, insures them against decline in their stability. This is because, even if some microbial species fail to deal with environmental change, others might not necessarily be affected similarly. Our findings demonstrate that phylogenetic diversity is the main controlling factor of the variation in stability across sites and requires more attention in sustainable forest management.
The Data‐Limited Methods Toolkit (DLMtool): An R package for informing management of data‐limited populations

A simulation‐based approach known as management strategy evaluation (MSE) is increasingly used by resource managers to identify management procedures that are robust to uncertainties in system dynamics. The majority of global fish populations are data limited and there is large uncertainty over their population and exploitation dynamics. The Data‐Limited Methods Toolkit (DLMtool) is an R package that allows for rapid and flexible MSE specification. The package consolidates a large number of existing data‐limited management procedures and allows for rapid MSE testing of new approaches. The DLMtool package has supported transparent and rigorous decision‐making for a number of data‐limited populations, identifying robust management procedures and revealing performance trade‐offs.
Complete mitochondrial genome of the Endangered fish Anabarilius liui yalongensis (Teleostei, Cyprinidae, Cultrinae)

Abstract We describe the complete mitochondrial genome of the Endangered fish Anabarilius liui yalongensis. It is a circular molecule of 16,608 bp in size, and all genes show the typical gene arrangement conforming to the vertebrate consensus. The cytochrome c oxidase subunit I (COI) sequence of A. liui yalongensis and other 21 species from 14 genera were used for phylogenetic analysis by Bayesian inference and maximum likelihood methods. The topology demonstrated that the A. liui yalongensis clustered with A. grahami are closely to Hemiculter branch within the subfamily Cultrinae.
Late flowering time enhances insect pollination of turnip rape

1. Ecological intensification has been proposed as a strategy to mitigate the impacts of conventional intensive land use on pollinators and insect pollination. However, research has concentrated on the effects of land management on pollinator abundance and diversity, while studies directly measuring pollination services are still lacking for many crops and regions. 2. This study examines the effects of landscape heterogeneity, pesticide use intensity and flowering time on insect pollination of turnip rape Brassica rapa ssp. oleifera, a major oil crop at high latitudes. The field experiment included monitoring pollinator visits on turnip rape flowers and measuring yield in 34 spring-sown turnip rape fields in Southern Finland. The fields were situated in two landscape types that differed in the cover of arable land and represented independent gradients of pesticide use intensity and flowering time. 3. Based on flower visits and number of seeds per silique, turnip rape was best pollinated in fields with late flowering time. The result suggests a temporal mismatch between crop flowering and the availability of pollination service in early sown fields. The increase in flower visits during summer was steeper among fields
Malicious URL(s) classification

Malicious URLs are a serious threat to the realm of online security and are one of the most fundamental ways to attack any online user. URL(s) can work as a primary source for distribution of malware/viruses over the internet which has led to an increasing urge for classification of URLs. To prevent users from being attacked, various anti-virus companies use black listing methods and block such URLs at a client end. However, there are millions of malicious URLs that are generated everyday and adding all these URLs in a blacklisting database becomes a monotonous method. Furthermore, it tends to lack newly generated URLs. To solve such problems, machine learning has grabbed attention in recent years to find out the hidden patterns from a dataset of URLs. Although it shows promise, it seems to be inefficient when the size of data is extremely large. This leads to the introduction of big data technologies where we apply machine learning algorithms in a distributed environment. In this research, we have critically compared the performance of traditional machine learning technologies with distributed modern machine learning technologies using Spark MLlib. We have used Logistic regression and Support Vector Machine algorithms in our model to determine the credibility of a URL. Our results conclude that each technique's performance is relative to the size of the data it is working on.
Relative Toxicity of Some Newer Insecticides against Mustard aphid, Lipaphis erysimi (Kalt.) on Gobhi sarson

Oilseed crops are generally one of the most important crops in the world. Rapeseedmustard is the major oilseed crop grown in various states of the country. This crop is the major source of income especially to the marginal and small farmers in rainfed areas. Because of its low water requirement (80-240 mm), rapeseed-mustard crop fits well in the rainfed cropping system. Rapeseed-mustard crop (Brassica sps.) is grown both in subtropical and temperate countries and it is the third most important oilseed crop in the world after soybean (Glycine max) and palm oil, Elaeis guineensis (Jacq.). The share of oilseeds is 14.1% out of the total cropped area in India, Rapeseed-mustard accounts for 3% of it (Kapila et al., 2012). In India, this crop is grown in diverse agro-climatic conditions ranging from north-eastern/north-western hills to down south under irrigated/rainfed, timely/late sown and mixed cropping. It is cultivated in 5.76 million hectares with an annual production of 6.82 million tones and average productivity of 1184 kg/ha which contributes 28.3% and 19.8% in world acreage and production (Anon., 2016a). India has the largest area and highest production of mustard. Currently, Rajasthan is the top International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 11 (2018) Journal homepage: http://www.ijcmas. com
Human Computer Interface Based on Tongue and Lips Movements and its Application for Speech Therapy System

The novel human computer interface is introduced, based on tongue and lips movements and using video data from a commercially available camera. The size and direction of the movements are extracted and can be used for setting cursor actions or to other relevant activities. The movement detection is based on convolutional neural networks. The applicability of the proposed solution is shown on the ASSISLT system [1], aimed to support speech therapy for adults and children with inborn and acquired motor speech disorders. The system focuses on individual treatment using exercises that improve tongue motion and thus articulation. The system offers an adjustable set of exercises which proper performance is motivated using augmented reality. Automatic evaluation of the performance of therapeutic movements allows the therapist to objectively follow the progress of the treatment.