Miracle-dz/UniFAR-FTUs huggingface dataset:
Adoption of NPS Fertilizer on Sorghum Crop Production by Smallholder Farmers in Gemechis and Mieso Districts of West Hararghe Zone, Oromia Regional State, Ethiopia

The adoption of inorganic fertilizer such as NPS which is concerned by development clients and government is different from one farmer to another farmer and this makes productivity of agricultural crops to vary from one plot to another plot due to socio-economic, institutional and other factors. Therefore, this study was intended to know the socio-economic factors that significantly affect utilization of inorganic fertilizer NPS. Primary data was collected from 201 sampled households of selected districts. Secondary data was collected from stakeholders related with production of sorghum and inorganic fertilizer NPS in the study areas. In the sampling procedure, two stage simple random sampling was used. In the first stage, kebeles were randomly taken from total kebeles in the two districts. In the second stage, households were randomly selected from the selected kebeles. Data was analyzed using descriptive, inferential statistics and econometric models methods of data analysis. In econometric models Double Hurdle model was use to know factors affect adoption decision of inorganic fertilizer NPS and intensity use of inorganic fertilizer NPS. Double Hurdle model result confirms that district of the household, education level, family size, extension visit, expectation of the coming rainfall by the household, number of farm plot owned, total farm land owned and off/non-farm income earned by the household significantly affect adoption decision inorganic fertilizer NPS. Double hurdle model result also reveals that, district of the household, livestock holding, number of farm plot owned, participation on agricultural training by the household significantly affect intensity use of inorganic fertilizer NPS. Government and concerned stakeholders should give attention on these significant socio-economic factors so that utilization inorganic fertilizer can be improved to sorghum crop productivity.
Peran Pembelajaran Matematika pada Penguatan Nilai Karakter Bangsa di Era Revolusi Industri 4.0

Era revolusi industri 4.0 adalah suatu era dimana teknologi informasi telah menjadi basis dalam kehidupan manusia, karena dipengaruhi oleh perkembangan internet dan teknologi digital. Tantangan yang harus dihadapi dalam perubahan hidup di era disrupsi ini adalah peningkatan kualitas sumber daya manusia yang mampu bersaing di era tersebut serta perlunya penguatan karakter bangsa. Pendidikan merupakan usaha sadar suatu generasi untuk membangun pengetahuan, sikap dan ketrampilan pada generasi berikutnya agar mereka siap menghadapi tantangan hidup pada jamannya. Makalah ini memberi penguatan bahwa nilai-nilai yang dibutuhkan generasi untuk hidup di era disrupsi ini dapat diperoleh melalui pembelajaran matematika. Penguatan ini dilakukan dengan mengkaji nilai-nilai yang terkandung dalam pendidkan secara umum, nilai nilai dalam matematika dan diimplemantasikan dalam pembelajaran matematika.
Subcloning and Nucleotide Sequence of the xylO/PUWCMA Region from the Pseudomonas putida TOL Plasmid pDK1

The TOL plasmids of Pseudomonas putida encode enzymes required for the oxidation of toluene and other related aromatic compounds. These genes are organized into two operons, the xylUWCMABN operon (upper), and the xylXYZLTEGFJQKIH operon (lower). Here we report the nucleotide sequence of a 7107 bp segment of the TOL pDK1 plasmid encoding the region just upstream of the "upper" operon through the genes encoding xylUWCMA. Sequence analysis, comparison of base-usage patterns, codon-usage patterns, and intergenic distances between genes help support the idea that the "upper" and "lower" operons have evolved independently in different genetic backgrounds and have only more recently been brought together in TOL and related catabolic plasmids.
In vitro development and characterisation of two clinically important biofilms

Environmental biofilms are abundant and represent the most prevalent growth mode of microorganisms. In humans, biofilms are frequently encountered and responsible for numerous infections which can be difficult to treat since biofilms tend to be more resistant to antimicrobial agents and host immune defences. The focus of this study was to characterise two biofilms associated with specific human infections, namely oral candidosis and chronic wound infection. In vitro biofilms using microorganisms from these infections were generated using microtitre plates, a constant depth film fermenter (CDFF) and reconstituted human epithelial tissue (RHE). Confocal laser scanning microscopy of Candida biofilms on RHE showed strain-dependent tissue invasion, with differences also evident in surface colonisation and Candida morphology. Hyphal elements invaded epithelial cells and exhibited budding within the tissues. A relationship between high Candidal tissue invasion and consistent expression of secreted aspartyl proteinase (SAP) genes 4-6 was found. There was no correlation between level of invasion and expression of phospholipase and agglutinin-like sequence (ALS) genes. These results demonstrate strain variation by Candida which relate to pathogenic potential. Biofilms of the chronic wound bacteria, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus oralis and Micrococcus luteus, showed species variation occurred in the extent of biofilm formation with antagonism evident in mixed species biofilms. Importantly, the pathogenic species of P. aeruginosa and S. aureus often inhibited biofilm formation by the commensal species (M. luteus and S. oralis). Susceptibility of wound bacterial biofilms to povidone iodine was reduced compared with planktonic cells. Up-regulation of biofilm genes by P. aeruginosa (alginate genes) and S. aureus (ica genes) was evident in the biofilm models. Extrapolation of results to chronic wound environments does require additional research on wound tissue, but the ability of the pathogenic species to antagonise commensal species could explain biofilm succession within a wound, possibly promoting a chronic wound phenotype.
Transmission efficiency and life table parameters of western flower thrips, Frankliniella occidentalis (Pergande) exposed to tomato spotted wilt virus-impatiens serotype

approved: Redacted for Privacy Peppermint, Mentha piperita 'Black Mitcham' was established as a host for tomato spotted wilt virus-impatiens serotype (TSWV-I). TSWV-I infection of peppermint, initially observed in a research greenhouse (Corvallis, OR), included stunting and downward curling of leaves accompanied by bronzing, and occasionally tip necrosis. Young leaves appeared either symptomless, deformed, or pale even under high nitrogen conditions. Older leaves had sunken, brownish-grey lesions. Bright yellow mottling was observed on newly mature deep green leaves. A begonia isolate of TSWV-I was transmitted to peppermint both mechanically and by western flower thrips, Frankliniella occidentalis (Pergande). Symptoms of TSWV-I infection were similar although only a faint yellow mottling was produced and only under cool temperatures (15°C). ELISA detection of virus distribution throughout the plant indicated infection was systemic. Bulked groups of thrips (5 thrips/sample) also tested positive for TSWV-I using ELISA. Transmission efficiency of 4, 6, 8, and 10 day old thrips adults given acquisition sources during the entire nymphal stage varied from 0-40% for thrips tested in pairs and 0-20% for single thrips (based on a 12 hour access feeding period). Adults 2 days old failed to transmit the virus. Western flower thrips exposed to TSWV-I had reduced survival and reproductive potential and slower development rates than unexposed thrips. Virusexposed thrips were 1.4 times as likely to die than unexposed thrips on a given day. Both individual and population reproductive potentials were significantly lower. Preoviposition period was extended in virus-exposed thrips. Development time from second instar to adult was 15% longer for virus-exposed thrips. This is the first report of altered population parameters in western flower thrips exposed to TSWV-I. Transmission Efficiency and Life Table Parameters of Western Flower Thrips, Frankliniella occidentalis (Pergande) Exposed to Tomato Spotted Wilt Virus-Impatiens Serotype
Change Process of Group Norms with Generational Change in a Small Group

Group norms are often revised or changed, although consistency and stability are desired when considering group management. The current study aimed to explore the process of group norm change by analyzing the minutes of meetings. Meeting minutes were coded by a psychologist and two graduate students of psychology. A total of 12 categories were identified: “Express determination in changing constitution”, “Ideal constitution,” “Informing current situation” “Changes from the past,” “Questions,”“Resolution of question by explanation,” “Statements for improvements” “Personal opinions,” “Understanding/agreements,” “Consents” “Conclusions,” and “Suspensions. ” The results of the current study demonstrated that 1) central group members’ perceptions of the gap between their ideals and the current situation led to a change in group norms in order to realize their ideals, and 2) group members changed the group norms taking into consideration the norms that had been passed down by former members and those that they would hand over to future members.
Mammalian Cell Biotechnology in Protein Production

Part 1 Genetic manipulation of mammalian cells: Heterologous expression of genes in mammalian cells, Hauser Permanent gene expression in mammalian cells - gene transfer and selection, Schlokar Vector for gene transfer and expression in animal cells, Sandig et al Aspects of gene transfer and gene amplification in recombinant mammalian cells, Wurm Isolation of recombinant cell clones exhibiting high-level expression of the introduced gene, Wirth Genetic engineering of antibodies and derivatives from mammalian cells,Weidle Safety evaluation of products derived from mammalian cell lines, Onions. Part 2 Biological aspects of animal cells: Metabolic control of animal cell culture processes, Wagner Glycosylation - a post-translational modification, Savage. Part 3 Cell cultivation technology: Bioreactors designed for animal cells, Tokashiki, Yokoyama Hydrodinamic properties in bioreactors, Chattopadhyay et al Kinetics and simulation of animal cell processes, Goergen et al On-line and Off-line process analysis, Scheper et al. Part 4 Down-stream processing: Principles of product extraction from cell culture and purification for pharmaceutical proteins, Walter, Allgaier.
IDEA's Teaching Essentials: Quick, Sound Student Feedback. IDEA Paper #77.

IDEA’s Teaching Essentials (TE) is a useful tool for gathering student feedback on how frequently an instructor exhibits each of seven behaviors that correlate most highly with student perceptions of course and teaching excellence. TE is appropriate for instructors who desire quick, sound student feedback on (a) displaying personal interest in students and their learning, (b) finding ways to help students answer their own questions, (c) demonstrating the importance and significance of the subject matter, (d) making it clear how each topic fit into the course, (e) explaining course material clearly and concisely, (f) introducing stimulating ideas about the subject, and (g) inspiring students to set and achieve goals which really challenge them. TE’s survey items are based on Chickering and Gamson’s Seven Principles for Good Practice in Undergraduate Education (1987), and they align with Hativa’s (2014) essential dimensions of effective teaching. Thus the instrument enjoys both empirical and theoretical support.
Physiological quality of soybean seed cultivars by osmoconditioning

Soybean cultivars present seeds of different physiological quality and they lose vigor and germinative potential during their permanence in the field after maturity. Therefore, this study was settled to evaluate the response ability to osmotic conditioning of seeds of six soybean cultivars – Confianca, UFV-16, Splendor, Garantia, UFVS 2005 and UFV-18 – harvested at the R8 stage and 15 and 30 days later. The cultivars were multiplied in the field, in a randomized complete-block design, with four replications. The osmotic conditioning of the seeds were carried out with a polyethylene glycol solution (PEG 6000), at -0,8 MPa, with 0.2% of Captan fungicide, at 20 °C, during 96 hours. Non conditioned seeds were used as control. The following characteristics were evaluated: first and final counting on germination test; seedling emergence rate and emergence speed index in the field; and electric conductivity. Harvest delay decreases seed germination and vigor, with different intensity, depending on the cultivar. The osmoconditioning reduces the leaching of solutes by the seed and positively affects the seed germination and vigor of all cultivar studied, more pronouncedly when seeds are much more weathered.
Review on Automatic Plant Identification Using Computer Vision Approaches

Plants are crucial resources on the Earth for ecological living habitat. However, the rapid loss of plant species has alerted the globe with the rising awareness of biodiversity conservation. ReThe need of plant identification provides an essential biologist information for plant research and development. It has brought significant impact on environmental conservation and exploration. Nevertheless, it requires species identification skills, high time consumption on study the species and usage of specific botanical terms. The knowledge of plant identification is not only for botanist and plant ecologists, but it is also useful for society, from professionals to the general public. The challenges of plant identification is the complexity of gaining plant species knowledge. Currently, with relevant technologies (digital cameras, mobile devices and remote access to databases) and computer vision techniques, it have created an automated plant identification to ease the society in plant identification. The aim of this paper is to document an analysis and comparison of studies between two types computer vision approaches for plant species identification and the features, i.e., shape, texture, colour, margin, and vein structure. It is useful to researchers in the fields for ongoing researches and comparable analyses of applied methods.
The effects of contact zone on phylogenetic characters in Persian Wheatear

The breeding ranges of Kurdish Wheatear (Oenanthe xanthoprymna ) and Persian Wheatear (Oenanthe chrysopygia ) in west and North West of Iran overlap and intermediate color variants can be found. It is possible that this supposed hybridization differs the characters of O.chrysopygia between contact zone and other distribution ranges in Iran. We aimed the survey of this possibility in this study. Field works carried out in spring and summer 2006 and 2007 and we found O.chrysopygia inside and outside of contact zone in west, northwest, east and center of Iran. Then, we used DNA sequences of two mitochondrial genes, NADH subunit 2 (ND2); 975 bp and cytochrome oxidase subunit I gene (cox1); 652 bp from 39 individuals and Bayesian, Maximum Likelihood (ML) also Maximum Parsimony (MP) methods to derive a phylogeny for comparison between O.chrysopygia inside and outside of contact zone. Our results confirmed O.chrysopygia in contact zone, well differentiated from O.chrysopygia in outside of contact zone. Furthermore, we confirmed the close phylogenetic relationships of supposed hybrid with O.chrysopygia despite a plumage coloration pattern close to O. xanthoprymna. Keywords-Wheatear;O.xanthoprymna;O.chrysopygia; supposed hybrid; hybridization; contact zone
Molecular Detection of Fungi in Foods and Feeds

Spoilage is a serious problem for the food industry because it renders products unacceptable for consumption. Spoilage of foods and feeds is often the result of microbial activity from a variety of organisms. The microbial flora that will develop depends very much on both intrinsic and extrinsic parameters, modes of processing and preservation, and implicit parameters (Deak 1991; Van der Vossen and Hofstra 1996). Yeasts and moulds can be found in a variety of environments because they can utilize a variety of substrates, and are relatively tolerant to low pH, low water activity, low temperature and preservatives. Consequently, although only a limited range of fungal species are responsible for the spoilage of a given food (Filtenborg et al. 1996), contamination of foods and feeds by yeasts and moulds has been extensively reported (Huis in’t Veld 1996). Fungi can contaminate foods and feeds at different stages including harvesting, processing and handling. Changes induced by spoilage of yeasts and moulds can be of a sensory nature, e.g., production of slime, pigmented growth, discoloration, rotting, development of off-odors and off-flavors. The most important aspect of food spoilage is, however, the formation of mycotoxins that may cause food poisonings. Although traditional morphological and physiological characters are fundamental parameters contributing to the identification of microorganisms in foods and feeds, these criteria may be influenced by environmental conditions. To supplement classical methods, a number of nucleic acid-based methods have been developed in the past few years. These methods have the advantage over phenotypic methods of not being influenced by environmental conditions of the cells since the nucleotide sequence of DNA remains constant during growth. This review focuses on molecular methods developed for direct detection of fungi in different foods and feeds. First, we will discuss two basic types of detection methods, those based on DNA hybridization, and those based on DNA amplification. In the second part of the chapter, the possible nucleic acid targets of direct detection methods will be discussed.
HIV-1 in the United Kingdom: population dynamics and genetic evolution

Background: Phylogenetic characterisation of local HIV-1 epidemics can be used to understand emerging transmission networks. We analysed subtype-unassigned sequences in the UK HIV Drug Resistance Database (UK HIV DRD) to map the emergence and origin of genetically diverse recombinant strains using phylogenetic analyses, near full-length sequencing of plasma HIV-1 and CD4 cell count decline. Methods: 55,556 genotyped pol sequences (protease amino acids 1-99, RT amino acids 1-234) were analysed for evidence of recombination. Near full-length single genome sequencing of plasma HIV-1 was performed on stored specimens from six patients with a putative A1/D novel recombinant strain. Recombination and phylogenetic analyses were performed using RIP, PhyML, jpHMM, Simplot, SCUEAL and FastTree v2.3. 1. Evolutionary analysis of putative novel recombinants was performed using Bayesian Evolutionary Analysis by Sampling Trees (BEAST). Geographic screening for additional instances of recombinant structures was performed using HIV BLAST and the Los Alamos National HIV database. Demographic data were available for 50/72 patients. CD4 cell count decline was assessed using linear regression. Results: The proportion of subtype-unassigned HIV-1 strains in the UK HIV DRD increased significantly during 1999-2008 (p=<0.01). 2,030 putative B-recombinant sequences were analysed for evidence of transmission of novel recombinant strains; 15 novel recombinant clusters comprising 94 individuals were identified. The proportion of intravenous drug users (IVDU), males and people of white ethnicity was significantly higher among novel recombinant clusters than among people infected with pure subtypes and recognised CRFs. Geographic screening showed co-circulation of novel strains in seven countries over three continents and import and export of novel strains from the UK was identified. Near full-length sequencing of six plasma specimens showed five patients sharing an identical A1/D strain; this was registered as CRF50_A1D and 67 further instances in the UK HIV DRD were identified. Geographic analysis showed close relation of component subtype A1 and D regions to East African strains; monophyletic clustering indicated a single introduction of this variant into the UK. Time scaled analysis showed a time to most recent common ancestor of approximately 1992. Demographic data showed the earliest CRF50 transmissions were confined to men who have sex with men (MSM), with subsequent transmissions to heterosexuals and IVDUs. Analysis of the sixth, complex, sequence demonstrated onward recombination of CRF50 with a subtype B strain (median divergence year 2000). CD4 cell count analysis suggested infections with CRF50 progressed in a similar manner to subtype B infections. Conclusions: Significant increasing genetic diversity of HIV-1 in the UK is linked to both UK and international transmissions among multiple exposure routes. These findings highlight the changing dynamics of HIV transmission in the UK and the converging of the two previously distinct MSM and heterosexual epidemics.
Characterization of the specificity and functions of the protein phosphatase Cdc14

Eissler, Christie L. Ph.D., Purdue University, December 2013. Characterization of the specificity and functions of the protein phosphatase Cdc14. Major Professor: Mark C. Hall. Protein phosphorylation is perhaps the most ubiquitous posttranslational modification in eukaryotes and recent studies suggest that upwards of 75% of human proteins are phosphorylated. Many proteins are phosphorylated at multiple sites, often controlled by multiple kinases and phosphatases. Multisite phosphorylation can differentially affect the functional and regulatory cellular outcomes. For example, dephosphorylation of a protein at a particular site may inhibit nuclear localization of a protein while dephosphorylation of a different site may be necessary for enzymatic activation of a protein. Thus, multisite protein phosphorylation can complicate our understanding of the biological significance and the functional consequences of protein phosphorylation. A clearer understanding of the functional consequences associated with an individual proteins phosphorylation status requires methods that can quantitatively monitor each phosphorylation site on a protein independent of one another. Here, I present a general method for quantitatively studying multisite protein phosphorylation. I demonstrate that label-free selected reaction monitoring (SRM) mass spectrometry is comparable to conventional assays for measuring reaction rates and steady-state kinetic parameters of phosphatases and kinases. Furthermore, I demonstrate that this method can be employed to measure the activity of an enzyme towards multiple substrates in a single reaction, suggesting that this approach is a useful tool for studying substrate specificity of kinases and phosphatases. I also demonstrate
Molecular plant biology : a practical approach

PART 1: GENE IDENTIFICATION 1. Classical mutagenesis in higher plants 2. Plant transfomrmation 3. T-DNA tagging 4. Transposion tagging methods in heterologous plants 5. Cloning plant genes by genomic subtraction PART 2: GENE ORGANIZATION 6. Approaches to gene mapping 7. Arabidopsis YAC, BAC and cosmid libraries 8. In situ hybridization to plant chromosomes and DNA fibres PART 3: LIBRARY SCREENING AND CDNA ISOLATION 9. PCR cloning approaches 10. Western and southwestern library screens 11. Complementation Cloning