Miracle-dz/UniFAR-FTUs huggingface dataset:
A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree. In the likelihood framework one commonly uses the marginal posterior probabilities of the character states, and the joint reconstruction of the most likely scenario. Both approaches are somewhat unsatisfactory. Marginal reconstructions provide users with state probabilities, but these are difficult to interpret and visualize, while joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences. We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts and the Brier criterion to associate each node in the tree to a set of likely states. A unique state is predicted in the tree regions with low uncertainty, while several states are predicted in the uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated to the same states and use graph visualization tools. The method is implemented in the PastML program and web server. The results on simulated data consistently show the accuracy and robustness of the approach. The method is applied to large tree comprising 3,619 sequences from HIV-1M subtype C sampled worldwide, which is processed in a few minutes. Results are very convincing: we retrieve and visualize the main transmission routes of HIV-1C; we demonstrate that drug resistance mutations mostly emerge independently under treatment pressure, but some resistance clusters are found, corresponding to transmissions among untreated patients.
EFFECT OF CONSUMER PERSONAL CHARACTERISTICS ON IMPULSE PURCHASE OF FRUIT JUICE AMONG SELECTED STUDENTS OF EKITI STATE UNIVERSITY, ADO-EKITI.

The study examines the effect of consumer personal characteristic on impulse purchase of fruit juice among selected students of Ekiti State University, Ado-Ekiti. Specifically, the study examined the effect of consumer personal characteristic (age, income and gender) on impulse purchase of fruit juice among selected students of Ekiti State University, Ado-Ekiti. A descriptive survey research design was adopted for the study. The total population was 2938 students of the three selected faculties (Management Sciences, Law and Medicine and Surgery) in Ekiti State University, Ado-Ekiti. 244 respondents were sampled using paler-calmorin and Calmorin (2006) computed sample size table. Primary data used for the study were gathered through the administration of structured questionnaire. Data gathered were analysed using multiple regression. The study found that the study found that age, gender and income has significant effect on impulse purchase of fruit juice among students of Ekiti State University, Ado-Ekiti. (t=3.327, t=-3.199 and t= 8.557, p<0.05). The study concluded that the constructs of consumer personal characteristic significantly affects impulse purchase of fruit juice among students of Ekiti State University, Ado-Ekiti. The study recommended that marketers, fruit juice producers and fruit juice business managers pay significant attention to customers’ need that are acceptable to students affordability.
A SUSTAINABLE PALM FRUIT VALUE CHAIN MODEL FOR SMALL-SCALE ACTORS IN NIGERIA

This theory’s model was driven by the need to empirically establish the possibility of smallholder’s in the Nigerian palm fruit value chain to compete with large-scale actors. Thereby, capturing a share of the consumer income which would promote sustainability. To achieve it, a theory submitted. Within this model, nineteen conceptual relationships were proposed to be contributors in the palm fruit value addition chain. A PLS-SEM technique was used to investigate the validity of these relationships. The primary data used for the investigation was surveyed from extension agents in Edo South agro-ecological zone of Edo State Nigeria. First, the article introduced the term Value Chain Theory. Next, it briefly familiarizes the readers with what structural equation modeling is all about, as well as its applications. Subsequently, the document preview literature on the pathways towards modeling a sustainable smallholder’s palm fruit’s value chain. Afterward, the researcher creates the path model for the drive of the investigation. Following that, the author ensured that the methodological approaches adopted in achieving the investigation were clearly specified. After which the results from the analysis ran were serially outlined and discussed. Last, but not least, the implications for the use of this model was highlighted and conclusion for the study was drawn. Thus, the author commended the robustness of the theory and, afterward, proposed a confirmatory test for the model. It was concluded that the tool exhibits prospects for promoting sustainability in the palm fruit value supply chain if properly adopted.
Astragalus wetherillii Jones (Wetherill's milkvetch) : a technical conservation assessment

ACKNOWLEDGMENTS This work benefited greatly from the help and generosity of several expert botanists and agency personnel, particularly Herbarium provided helpful information on Astragalus wetherillii specimens. Karin Decker is an ecologist with the Colorado Natural Heritage Program (CNHP). She works with CNHP's Ecology and Botany teams, providing ecological, statistical, GIS, and computing expertise for a variety of projects. She has worked with CNHP since 2000. Prior to this, she was an ecologist with the Colorado Natural Areas Program in Denver for four years. She is a Colorado native who has been working in the field of ecology since 1990, including four summers at the Rocky Mountain Biological Laboratory in Gothic, Colorado. Before returning to school to become an ecologist she graduated from the University of Northern Colorado with a B. Astragalus wetherillii (Wetherill's milkvetch). Photograph by William Jennings, used with permission. Status Astragalus wetherillii (Wetherill's milkvetch) is a local endemic whose global distribution is limited to Colorado west of the Continental Divide. Occurrences have been reported from approximately 50 sites in the Yampa, Colorado, Gunnison, Uncompahgre, and San Miguel river drainages. Documented occurrences include one site on the Rifle Ranger District of the White River National Forest and one on the Norwood Ranger District of the Grand Mesa, Uncompahgre, and Gunnison National Forests. Occurrences are also known from Bureau of Land Management lands, State of Colorado land, and private property. Astragalus wetherillii is considered a sensitive species in Region 2 of the USDA Forest Service. Due to its small global distribution, it is ranked G3S3 (vulnerable both globally and in the state, because of rarity or other factors) by NatureServe and the Colorado Natural Heritage Program. It is not listed as threatened or endangered under the Although Astragalus wetherillii is locally common in parts of its range and does not appear to be in significant decline, its entire global range is contained within the five river drainages mentioned above. Widespread threats in these drainages will affect the entire species. Based on the available information, there are several probable threats to A. wetherillii. In order of decreasing priority, these are road building and maintenance, off-road vehicle use, oil and gas development, livestock trailing, residential development, exotic species invasion, and global climate change. Without systematic tracking of population trends and conditions, and without a better understanding of the species' life cycle, there is the possibility that one or more of these factors …
Songs of wonder : an inquiry into wonder and magic in everyday and organisational life

This doctoral research explores which practices might support ‘wonder’ in everyday and organisational life. How do I live my life with a sense of wonder? How do I create spaces of wonder with and for others? How do I create a wonder-full research practice? As an action researcher (Reason & Bradbury, 2008) with a background in Appreciative Inquiry (Cooperrider & Srivastva, 1987), I have endeavoured to ‘live’ these questions myself through developing an approach for wholeheartedly loving and living questions. Specific methods I created to do so are daily morning walks, writing ‘moment-stories’ from within the experience of wonder and creating ‘temporary constellations of inquiry’ with others. Whereas some believe wonder is impossible because the world is disenchanted, I followed Bennett’s (2001) approach of enchantment by emergence by challenging the discourse of disenchantment individually. Building on Carson (1956/1998), I think of wonder as ‘seeing the extraordinary within the ordinary’ and found this seeing requires a continuous effort and benefits from routines and rituals as a daily reminder and opportunity to wonder. I distinguish between wonder as a way of seeing you can cultivate and ‘moments of magic’ that strike unexpectedly. ‘Windows’ in time when I feel fully alive in a world bursting with life. I learned these potentially transformative moments cannot be forced, predicted or replicated and therefore argue to approach them ‘obliquely’ – by holding the intention and possibility of magic in the corner of your eye. And instead focus on the practices that help you to wonder on a day-to-day basis. I learned the most important thing I can do as a practitioner to invite others to wonder is to continue to actively and wholeheartedly live my own questions. This allowed me to create the conditions for wonder and magic through showing up differently myself and ‘embodying the container’. I also learned that giving words to wonder through writing and sharing moment-stories can increase the importance and possibility of wonder for myself and others.
Optimization of the pasteurization of Saba senegalensis nectar

Wild neglected fruits as are known for their beneficial effects on health and the fight against malnutrition. This is the case in Senegal of the fruits of Saba senegalensis wich are consumed more and more in the form of nectar whose nutritional and organoleptic qualities must be preserved. The objective set by this work is to optimize the pasteurization of the nectar in order to preserve its whole quality.The minimum pasteurizing value (VP) is determined and then different pasteurization scales to obtain this VP are tested. The vitamin C of the obtained nectars is monitored for 60 days at 4; 20; 30 and 37 ° C. A 50-minute VP gives microbiological stability for two months at 4 ° C and retains the nutritional qualities of the nectar. Thus, the optimal 73 ° C / 16 min scale is used for this fruit nectar because it preserves 63.38% of the vitamin C. The use of the Ball, Arrhenius and Eyring models during the tests makes it possible to predict adequately the losses of vitamin C. The 73 ° C / 16min scale better retains the nutritional and organoleptic qualities of the nectar of Saba senegalensis.
Inland Coal Mine Settling Pond as a Habitat for the Brackish-Water Plant Ruppia maritima

ABSTRACT The research conducted in settling ponds located in the coal basin in Upper Silesia (southern Poland), detected in one of them presence of the widgeon grass Ruppia maritima. Currently, it is the only inland site of this species in Poland. The widgeon grass creates underwater meadows in the shore zone of the settling pond and it grows in dense communities together with the common reed Phragmites australis in the coastal zone. Apart from these two plants, no other species were found. The morphological features of the vegetative and generative organs of the studied population of R. maritima is similar to those that have been reported from Europe. The bottom of the pond is atypical for R. maritima – it is covered by mine waste. The water of the settling pond has a high salinity and the water chemistry corresponds to the more natural environments that are inhabited by widgeon grass. This substitute habitat, which imitates the natural environment of R. maritima contributes to the good development of these species. However the studied settling pond offers unstable conditions due to the ongoing mining activity and requires permanent monitoring.
Local online learning in recurrent networks with random feedback

A longstanding challenge for computational neuroscience has been the development of biologically plausible learning rules for recurrent neural networks (RNNs) enabling the production and processing of time-dependent signals such as those that might drive movement or facilitate working memory. Classic gradient-based algorithms for training RNNs have been available for decades, but they are inconsistent with known biological features of the brain, such as causality and locality. In this work we derive an approximation to gradient-based learning that comports with these biologically motivated constraints. Specifically, the online learning rule for the synaptic weights involves only local information about the pre- and postsynaptic activities, in addition to a random feedback projection of the RNN output error. In addition to providing mathematical arguments for the effectiveness of the new learning rule, we show through simulations that it can be used to train an RNN to successfully perform a variety of tasks. Finally, to overcome the difficulty of training an RNN over a very large number of timesteps, we propose an augmented circuit architecture that allows the RNN to concatenate short-duration patterns into sequences of longer duration.
Species composition, seasonal prevalence and flavivirus occurrence of mosquitoes in Daegu and Gunwi, South Korea during the period of 2015–2016

As the vector‐borne diseases rapidly increased due to climate change, we investigated the incidence of flavivirus occurrence among female mosquito species in urban and rural study sites in Daegu and Gunwi, South Korea using Realtime PCR. We collected more individuals and more species of mosquito in 2016 than in 2015. In 2015, we recorded a total of 22,033 mosquitoes (Trap Index, 224.8) representing 10 species from 5 genera, whereas in 2016, a total of 27,137 mosquitoes (Trap Index, 278.7) representing 13 species from 6 genera were collected. The number of mosquitoes in 2016 was higher in all study sites, except in the migratory bird habitats where the number decreased. Of the 14 species collected over the two years, Aedes vexans nipponii and Anopheles spp. were dominant in the cowsheds in rural farmland; Culex pipiens complex, in urban residential areas; and, Anopheles spp. and Cu. pipiens complex in migratory bird habitats caught in a black light trap. Cu. pipiens complex and Ae. albopictus in urban parks and Ae. albopictus and Armigeres subalbatus in migratory bird habitats were the dominant species caught in BG‐sentinel traps. We found that the number of mosquitoes was highest during July–September. We analyzed 1,725 pools to detect flavivirus, where Chaoyang virus was detected among Ae. vexans niponii collected from cowsheds in rural farmland in 2016. The increased number of mosquitoes recorded in 2016 was mainly due to increased temperatures in the study areas, and reflected the change in study sites.
Trophic patterns and home‐range size of two generalist urban carnivores: a review

Foxes and cats are the most abundant medium-sized urban carnivores. To date, however, there has been a lack of effort to synthesize data on the spatial and trophic resources used by these two carnivores, despite the importance of this information for assessing their similarity and roles in urban food webs. In this paper, we first synthesize all available information on the trophic patterns and home-range size of these two predators based on a total of 91 studies. Second, we conduct statistical analyses to test the influence of environmental and biological variables such as regional differences, habitat characteristics, age, and sexual status on their home-range size and diet patterns within urban habitats, and then evaluate the methods used to investigate these components. Our findings highlight the lack of studies that simultaneously monitor the diet and home-range size of both predators within urban habitats. To the best of our knowledge, this is the first study to compare fox and cat home-range size and diet. Foxes exhibited larger ranges than cats, while intact cats showed larger home ranges than desexed cats. Diet diversity obtained for both predators confirmed their trophic plasticity within urban habitats. Both predators consumed fewer mammals and invertebrates in highly disturbed habitats compared to medium ones. We also found that the procedure of data acquisition significantly influenced fox and cat home-range sizes. In terms of diet, the type of recovered samples had a significant effect on the diet composition of both predators. To improve our understanding of the relative impact of these two urban carnivores on urban wildlife, we recommend simultaneously studying both species in future studies. Moreover, methodological standards for both diet and home-range size studies are needed to allow comparisons.
La investigación acción y el desarrollo de competencias para el ejercicio del derecho.

The action research operativizes the characteristics of the qualitative paradigm, gives relevance to a micro-social perspective, the researcher is an eyewitness of what he studies, and its purpose is not to explain but to understand; it analyzes in depth the meaning of the particularities of social life. Considering the importance of these particularities, we sought to describe the competencies acquired by the students of the action research subject, after the April-August 2019 academic period. The results showed that most of the informants acquired a memoristic learning that limits the development of the competencies required for the profile of the lawyer, which is explained by the weight of the positivist paradigm and by the complexity of internalizing new philosophical and theoretical perspectives.
Hubungan Kemandirian Belajar dengan Kemampuan Pemecahan Masalah Matematis

Penelitian ini dilatarbelakangi oleh kemampuan pemecahan masalah matematis dan kemandirian belajar peserta didik yang masih rendah dalam menyelesaikan masalah matematis. Tujuan penelitian ini adalah untuk mengetahui hubungan antara kemandirian belajar dengan kemampuan pemecahan masalah matematis peserta didik SMK pada materi program linear dua variabel. Penelitian ini termasuk jenis penelitian korelasional yang dilakukan pada kelas X Farmasi Klinis dan Komunitas dengan 31 orang peserta didik. Instrumen dalam penelitian ini adalah angket kemandirian belajar dan soal tes kemampuan pemecahan masalah matematis. Analisis data yang digunakan pada penelitian ini meliputi analisis korelasi product moment untuk mengukur hubungan antara kemandirian belajar dengan kemampuan pemecahan masalah matematis. Hasil penelitian menunjukkan bahwa terdapat hubungan positif antara kemandirian belajar dengan kemampuan pemecahan masalah matematis sebesar 0,764 dengan signifikansi 0,000 < 0,05. Hal ini menunjukkan bahwa kemandirian belajar dapat dijadikan sebagai salah satu faktor yang dapat mempengaruhi kemampuan pemecahan masalah matematis peserta didik. Jika kemandirian belajar yang dimiliki peserta didik tinggi, maka kemampuan pemecahan masalah peserta didik baik, namun jika kemandirian belajar peserta didik rendah, maka kemampuan pemecahan masalahnya kurang baik
Multiplex Real-Time PCR in Bovine Mastitis Diagnostics

Mastitis is the most common and economically damaging production disease of dairy cows. In the majority of cases it is induced by intramammary infection with a pathogen. Identification of mastitis-causing pathogens enables treatments to be targeted appropriately, avoiding unnecessary antimicrobial treatments, and enabling design of the best possible herd level management protocols. Diagnosis of bovine IMI has been traditionally based on microbial culture of aseptically taken quarter milk samples. Due to the requirements of modern dairy production and development of molecular technologies, milk samples can be examined for target pathogens with DNA-based methods such as multiplex real-time PCR assays. Despite several years of routine use of PCR assays in some countries, scientific knowledge concerning interpretation of the results is sparse. This dissertation focuses on providing new information for diagnosing bovine mastitis using multiplex real-time PCR. In order to accomplish that, first a commercial multiplex real-time PCR assay was compared with the current reference method, conventional culture (I). It showed that PCR was a reliable diagnostic method for Staphylococcus aureus, but less reliable for diagnosing true non-aureus staphylococci infections. In an experimental challenge study (IV), elimination of Staphylococcus epidermidis and S. simulans was followed with PCR in addition to conventional culture. The results showed that PCR yielded target-positive results for several days after the culture results were negative. Subsequently, the time of sampling related to the onset of inflammation may be of importance when interpreting the PCR results. Secondly, quarters with suspected mastitis were sampled using two experimental techniques, in addition to the conventional aseptic technique (II, III), and examined with multiplex real-time PCR. In the needle technique, the whole teat and teat area were bypassed. With the cannula technique, the teat orifice and the teat canal were bypassed. The results showed that samples taken with alternative techniques were of better hygienic quality. We also reported that over half of the non-aureus staphylococci findings in our PCR results originated from sites other than the mammary gland. A diagnosis of a true IMI or mastitis, with possible outcome of an antimicrobial treatment course for the animal, cannot be based solely on a PCR result, but must be combined with all the available information about a cow`s history, symptoms, changes in milk and indicators of inflammation. Some microbes detected with PCR can be considered to be contaminants, especially when present with low levels of DNA. If the signs of the cow or the degree of udder inflammation do not fit the usual signs caused by the pathogen detected, the possibility of contamination should be considered.
Sparse Bayesian Learning for Predicting Phenotypes and Ranking Influential Markers in Yeast

Genomic selection and genome-wide association studies are two related problems that can be applied to the plant breeding industry. Genomic selection is a method to predict phenotypes (i.e., traits) such as yield and drought resistance in crops from high-density markers positioned throughout the genome of the varieties. In this paper, we employ employ sparse Bayesian learning as a technique for genomic selection and ranking markers based on their relevance to a trait, which can aid in genome-wide association studies. We define and explore two different forms of the sparse Bayesian learning for predicting phenotypes and identifying the most influential markers of a trait, respectively. In particular, we introduce a new framework based on sparse Bayesian and ensemble learning for ranking influential markers of a trait. Then, we apply our methods on a real-world Saccharomyces cerevisiae dataset, and analyse our results with respect to existing related works, trait heritability, as well as the accuracies obtained from the use of different kernel functions including linear, Gaussian, and string kernels. We find that sparse Bayesian methods are not only as good as other machine learning methods in predicting yeast growth in different environments, but are also capable of identifying the most important markers, including both positive and negative effects on the growth, from which biologists can get insight. This attribute can make our proposed ensemble of sparse Bayesian learners favourable in ranking markers based on their relevance to a trait.