Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Fingerprinting of Potato Varieties

The objective of this project was to learn how to extract potato DNA and examine the differences between potato varieties at the DNA level. Potato plants were used as a source of DNA for a study of the comparison of DNA from different potato varieties. Two test potatoes (P11-1 and P23-1) were used to standardize the fingerprinting procedure that gave the best results. Ten other potatoes were then planted; the DNA was extracted using the Cetyltrimethylammonium Bromide (CTAB) method, and individual potatoes were compared by Random Amplified Polymorphic DNA (RAPD) technique. The tested potato varieties were found to vary a lot. The RAPD results were clear and easy to compare. It was concluded that DNA fingerprinting is a powerful technique to study the genetic variation between plant varieties and can be used for plant improvement.
CNT-Cache: an Energy-Efficient Carbon Nanotube Cache with Adaptive Encoding

Carbon Nanotubu field-effect transistor (CNFET) that promises both higher clock speed and energy efficiency becomes an attractive alternative to the conventional power-hungry CMOS cache. We observe that the CNFET-based cache constructed with typical SRAM cells has distinct energy consumption when reading/writing 0 and 1 from/to it. For instance, the energy consumption of writing 1 to an SRAM cell is almost 10X higher than writing 0. With this observation, we propose an energy-efficient cache design called CNT-Cache to take advantage of this feature. It predicts the cache line access pattern based on the latest cache line access history. On top of the prediction, it decides the optimal cache line encoding to match the cache operation preferences at runtime. According to our experiments on a set of benchmark programs, the optimized CNFET-based D-Cache reduces the dynamic power consumption by 22.2% on average compared to the baseline CNFET cache.
Continuous Mammalian Cortical Area Development Model: Transforming From Qualitative To Quantitative Model

: The understanding of mammalian cortical area development network has long been a core objective in Systems Biology. The cerebral cortex is spliced into many functionally distinct areas. The evolution of these areas during neural growth is relied on a set of genes expression patterns. For instance, through the anterior-posterior axis, gradients of set of genes such as Fgf8, Emx2, Pax6, Coup-tfi, and Sp8 control the role in specifying a real identity. The Knowledge about this network is mainly of qualitative nature and incomplete. Therefore, we utilized a computational method to understand the complex dynamic interactions behavior between the aforementioned genes. There is a need to understand which interactions, and other combinations of interactions would be appeared in networks that mimic the anterior-posterior expression patterns. In addition, a continuous concentration measurements are considered as significant indicators for proteins activities. The concentration level during the interaction can provide more insight to understand system activities and supports both of diagnosis and drugs treatment studies. Thus, to achieve this task, herein, we present a two-step approaches to facilitate the computational model. The first step is employing a Boolean network model since the available knowledge in qualitative form, this model mimics the genes interactions. The Boolean model treats expression levels as Boolean since the nature of the expression data is currently available in the qualitative form. However, even the discrete model is a powerful tool to study and understand the dynamic behavior of genes interaction, but it can never provide detailed time courses of concentration levels. Therefore, in the second step, we transformed the discrete-Boolean model to continuous simulation to reproduce a continuous protein concentration. We engaged a standard method such as multivariate polynomial interpolation to transform the logic operations to ordinary differential equations model (ODE).
The face-on views of X-shaped “bulges” - boxy features in the central parts of bars

Abstract Boxiness associated with the morphology of the central parts of bars, is a feature usually encountered in the edge-on profiles of galaxies, or galactic models. However, there are cases where “boxy” isophotes are observed also in the central parts of nearly face-on bars. I summarize here some dynamical mechanisms that support boxy orbits in the central bar regions on the equatorial plane of the disks, or orbits with boxy projections on it. Such orbits could describe the dynamics of face – on boxy “bulges”.
Transverse bar/bulge kinematics with Gaia and VVV

Abstract We present new results on the Galactic bar/bulge transverse velocity structure using Gaia and the VISTA Variables in Via Lactea (VVV) survey. Gaia is complemented in high extinction regions by the multi-epoch infrared VVV observations for which derived relative proper motions can be tied to Gaia’s absolute frame. We extract kinematic maps (both 2D and 3D) of the Galactic bar/bulge, from which we measure the pattern speed of the bar using a novel technique. We focus on the evidence of an X-shaped bulge from the kinematic maps.
Effect of probiotics Lactobacillus paracasei GKS6, L. plantarum GKM3, and L. rhamnosus GKLC1 on alleviating alcohol-induced alcoholic liver disease in a mouse model

BACKGROUND/OBJECTIVES Heavy alcohol consumption causes the development of alcoholic liver disease (ALD), a neglected but important public health problem. Many studies have pointed out that probiotics could improve gut health, which is also considered to be a cause of ALD. Therefore, this study screened the probiotics, Lactobacillus casei GKC1 (GKC1), L. fermentum GKF3 (GKF3), Bifidobacterium lactis GKK2 (GKK2), L. rhamnosus GKLC1 (GKLC1), L. paracasei GKS6 (GKS6), and L. plantarum GKM3 (GKM3), for their potential benefits in alleviating ALD for applications to disease prevention. SUBJECTS/METHODS C57BL/6N mice were divided into 8 groups (n = 6 in each): normal control, positive control (alcohol-diet fed), and treatments of feeding probiotics GKC1, GKF3, GKK2, GKLC1, GKS6, and GKM3 under an oral dose 0.82 g/kg B.W. per day by oral gavage. The experiment was conducted for 8 weeks, and the concentrations of alanine aminotransferase (ALT), aspartate aminotransferase, triglyceride (TG), and total cholesterol (TC) in mice were measured. The glutathione (GSH), catalase (CAT), and histology were analyzed after sacrifice. RESULTS The results showed a decrease in the serum ALT, liver TG, and liver TC levels in the GKS6, GKM3, and GKLC1 groups compared to the positive control. In addition, the decreasing GSH and CAT levels were inhibited in the GKS6 and GKM3 groups. The histopathological results showed that all probiotics could reduce the accumulation of liver fat. Furthermore, there was a significant difference in GKLC1 with lower stomach damage compared to the alcohol-fed mice without any addition of probiotics. CONCLUSIONS GKLC1, GKS6, and GKM3 can be used as supplements for alleviating the development of ALD.
Lexichrome: Text Construction and Lexical Discovery with Word-Color Associations Using Interactive Visualization

Based on word-color associations from a comprehensive, crowdsourced lexicon, we present Lexichrome: a web application that explores the popular perception of relationships between English words and eleven basic color terms using interactive visualization. Lexichrome provides three complementary visualizations: "Palette" presents the diversity of word-color associations across the color palette; "Words" reveals the color associations of individual words using a dictionary-like interface; "Roget's Thesaurus" uncovers color association patterns in different semantic categories found in the thesaurus. Finally, our text editor allows users to compose their own texts and examine the resultant chromatic fingerprints throughout the process. We studied the utility of Lexichrome in a two-part qualitative user study with nine participants from various writing-intensive professions. We find that the presence of word-color associations promotes awareness surrounding word choice, editorial decision, and audience reception, and introduce a variety of use cases, features, and opportunities applicable to creative writing, corporate communication, and journalism.
Dataset Paper Discovery of MicroRNAs in Cardamom (Elettaria cardamomumMaton) under Drought Stress

MicroRNAs (miRNAs) are endogenous, 19–24-nucleotide-long, noncoding RNAs found in animals, plants, and some viruses. Drought is one of the major limiting factors that negatively affect productivity of plants. To date, nothing is known about the regulatory roles of miRNAs in response to drought stress in cardamom. Cardamom collected from the natural forest area in Therakkudi in the Idamalayar forest range was selected for the study. Total RNA was isolated from leaves and stems of control and drought treated cardamom plant, which was used for library construction. Ion torrent sequencing of the two small RNA libraries prepared from plants raised under well irrigated and drought stressed treatments, respectively, created 3,938,342 and 4,083,181 primary reads. A total of 150 conserved and 20 novel microRNAs were identified from both the control and the treated libraries. Discovery of 17 differentially expressed miRNAs under drought stress suggests that these might have been involved in various biological processes to improve plant tolerance to water stress. This study is the first report of drought responsive miRNAs and their targets in cardamom. The outcome of this research could provide insights into the miRNA based regulatory mechanisms in response to drought stress in monocot plants.
ModelSpeX: Model Specification Using Explainable Artificial Intelligence Methods

Explainable artiﬁcial intelligence (XAI) methods aim to reveal the non-transparent decision-making mechanisms of black-box models. The evaluation of insight generated by such XAI methods remains challenging as the applied techniques depend on many factors (e.g., parameters and human interpretation). We propose ModelSpeX, a visual analytics workﬂow to interactively extract human-centered rule-sets to generate model speciﬁcations from black-box models (e.g., neural networks). The workﬂow enables to reason about the underlying problem, to extract decision rule sets, and to evaluate the suitability of the model for a particular task. An exemplary usage scenario walks an analyst trough the steps of the workﬂow to show the applicability.
Climate change and agricultural productivity

Agriculture is the economic sector that is most vulnerable to climate change. According to the latest estimates, farmers’ adaptation of farm production to climate change is inevitable. The climate attributes that are expected to have the most direct impacts on agricultural productivity are the rise in temperature, the change in the frequency and intensity of precipitation and of extreme weather phenomena, and the increase in the level of CO2 available for photosynthesis. This paper analyzes the economic costs of climate change in Greek agricultural productivity during the last thirty years and discusses the implications for policymakers and for agricultural research. Empirical evidence suggests that climate change is already present and has a significant impact on agricultural productivity. Farmers need to adapt to the expected impacts of climate change in order to maintain their standard of living. The adaptation of agriculture to climate change involves both the restructuring of crops, as well as changes in cultivation practices. Policies must take into account the multidimensionality of modern agriculture and the importance of sustainable agricultural development.
NFL Betting Market Efficiency, Divisional Rivals, and Profitable Strategies

PurposeThis paper aims to examine market inefficiencies in the National Football League (NFL) betting market from the 2003 season to the 2016 season.Design/methodology/approachThe author examines the impact that division rivals and previously known determinants of inefficiencies have on the current NFL gambling market.FindingsThe results show that games against division rivals have a lower chance of the home team covering the spread and the chance the game will result in an over. This result demonstrates that the sportsbooks underestimate the familiarity that teams have with each other’s players, coaches and tendencies from playing each other twice per year. Moreover, using this result in conjunction with previous known inefficiencies, the author puts forth a model to test out of sample predictions. The results from these tests show profitable strategies in the point spread and totals market with a win rate of nearly 57 per cent.Originality/valueOverall, this paper demonstrates inefficiencies in the NFL betting market that future bettors may be able to take advantage of.
Relationship Between Employer Branding And Employee Citizenship Behavior: Brand Centered HRM As A Mediator

To grapple with challenges that market faces today organizations including Telecommunication sector are thoughtful about to strengthen their performance of organization and stand out in market at top of the leading well reputed organization. Therefore based on liter ature regarding employer branding that highlights the several studies that provide suggestions of some most important and effective factors of employer branding that leads towards the employee citizenship behavior but there are certain factors and inconsistent findings that need to be further investigated with help of mediating role of brand centered HRM . Through mediating role of brand centered HRM further provides clarity in enhancing employee‘scommitment with the organization.Taking into consideration this phenomenon suggested the conceptual framework representing the employer branding dimensions,brand centered HRM andemployee citizenship behavior that demonstrate the success of organization. This paper attempts to generate very useful insights about the performance of telecommunication sector that how telecommunication sector of Pakistan branding themselves as aexceptional workplace to work and earns reputation in the perception of current and prospective personnel, greater the company‘s reputation, greater the employee citizenship behavior.From the perspective of employee citizenship behavior, conceptual discussions linked to employer branding that can contribute to our understanding of citizenship behavior of employees.Therefore, thispaper attempts to examine the role of brand centered HRM as significant contributor in employer branding and leads towards employee citizenship behavior.
Cryptic diversity concealed in the Andean cloud forests: two new species of rainfrogs (Pristimantis) uncovered by molecular and bioacoustic data

Two new species of frogs previously confused with Pristimantis calcarulatus are identified using molecular phylogenetics and described using an integrative taxonomic approach. The species are distributed in montane cloud forests of the northwestern Ecuadorian Andes. Pristimantis pahuma n. sp. and Pristimantis cedros n. sp. differ from their closest relatives by strongly supported reciprocal monophyly in mitochondrial genetic data (16S). Additionally, the genetic distance among P. cedros n. sp. , P. pahuma n. sp. and P. calcarulatus (sensu stricto) is 7.1–9.5%. The advertisement call of P. pahuma n. sp. also differs from that of P. calcarulatus; the former emits single-note calls irregularly, whereas P. calcarulatus always calls in a series of 8–24 notes (calls for P. cedros n. sp. not recorded). Morphologically, the three species are almost undistinguishable; however, P. cedros n. sp. differs in life by having an iris with more numerous and smaller black reticulations, whereas the other two species have larger and fewer reticulations. Biogeographically, P. cedros n. sp. is separated from P. pahuma n. sp. and P. calcarulatus by the climatically dry and low elevation Río Guayllabamba Valley, which acts as a strong barrier to dispersal in these frogs. The results of this and other studies suggest that the true species richness of Pristimantis in the Andes is vastly underestimated. This underestimation may lead to declining protection for such cryptic species, many of which have smaller ranges than previously assumed. Species distributed across potential geographic barriers should be studied to detect the existence of cryptic species.
Avian Geophagy and Soil Characteristics in Southeastern Peru

ABSTRACT We observed ten species of psittacids, three species of columbids, and two species of cracids consuming soil from banks of the lower Tambopata River in southeastern Peru. Our study used observations and soil analyses from eight exposed riverbank sections to test the predictions of three models to determine why birds consume clay: mechanical aid to digestion (grit), adsorption of dietary toxins, and mineral supplementation. We found that preferred soils were deficient in particles large enough to aid in the mechanical breakdown of food and help digestion. Percent clay content and cation exchange capacity (CEC), both predicted to correlate with adsorption of toxins, did not differ between used and unused sites as had been found in a similar study. Instead, preferred soils were more saline and had higher concentrations of exchangeable sodium. This suggests that the choice of soils at our site was based primarily on sodium content. Birds may be using the heavy, plastic texture of soils rich in clays and high in exchangeable sodium as a proximal cue for soil selection. Our findings suggest that avian soil selection decisions depend on the range of available soil characteristics.
SelfE: Gene Selection via Self-Expression for Single-Cell Data

Single-cell RNA sequencing has been proved to be advantageous in discerning molecular heterogeneity in seemingly similar cells in a tissue. Due to the paucity of starting RNA, a large fraction of transcripts fail to amplify during the polymerase chain reaction cycle. This gets compounded by trivial biological noise such as variability in the cell cycle specific genes. As a result expression matrix obtained from a single-cell study is highly sparse with a large number of missing values. This hinders downstream analysis of single-cell expression data. It has been observed that feature engineering significantly improves the analysis outcomes. Feature extraction methods such as principal component analysis and zero-inflated factor analysis have been shown to be useful for subsequent steps of data analysis including clustering. However, too little or no visible efforts have been observed for developing feature selection techniques, which offer transparency for the analyst's consumption. We propose SelfE, a novel <inline-formula><tex-math notation="LaTeX">$l_{2,0}$</tex-math><alternatives><mml:math><mml:msub><mml:mi>l</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mo>,</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:msub></mml:math><inline-graphic xlink:href="rai-ieq1-2997326.gif"/></alternatives></inline-formula> -minimization algorithm that determines an optimal subset of feature vectors that preserves sub-space structures as observed in the data. We compared SelfE with the commonly used feature selection methods for single-cell expression data analysis.
Habitat and Annual Variation in Arthropod Abundance Affects Blue Tit Cyanistes caeruleus Reproduction

Abstract. Arthropod assemblages living in tree canopies in two habitat types — a rich woodland and poor parkland were studied in 2003–2005 as a background for describing the dynamics of caterpillars; the study system was located in central Poland. Caterpillars, the optimal food of breeding tits, varied in abundance between both habitats and years. The peak abundance of caterpillars was at least 3 times higher in the woodland than in the parkland habitat. There were also pronounced differences in caterpillar production between years, with every consecutive year during 2003–2005 being trophically worse than the previous one. The Blue Tits' timing of breeding coincided roughly with the timing of caterpillar abundance in particular years. Mean clutch size corresponded strictly to the inter-habitat and inter-year pattern of variation in caterpillar availability, suggesting adaptive responses in Blue Tit reproduction to food resources.
Some aspects of the ecological niche of chironomids associated with submersed aquatic macrophytes in a tailwater

High values of chironomids' production were recorded and analysed in the tailwater of a dam reservoir located on a large river. The values resulted from submersed aquatic macrophytes (SAM) patches that appear on the bottom in summer, as an effect of a specific discharge pattern through the dam. Abundant and taxonomically rich chironomid assemblages develop there, but their populations display different spatial and trophic preferences, which are the main topic of our interest here. We focused on dominant taxa of Orthocladius/Cricotopus spp. , Chironomus riparius Meigen and Glyptotendipes cauliginellus (Kieffer), whose abundance and biomass exceeded 90% of all chironomids inhabiting the SAMs. The developmental time of their aquatic stages (cohort production interval − CPI) and thus production, and production to biomass ratio (P:B) differed considerably. A P:B ratio of 13.8 was estimated for the first taxon, a mid-body size scraper living on stems and leaves of SAMs. In contrast, P:B ratios of 5.2-7.7 were assessed for the second and third taxa, rather large body size benthic gathering collectors inhabiting the roots of SAMs. The main food categories of gathering collectors were particulate organic matter trapped by the roots, while scrapers fed on algae developing on leaves and stems.
Phylogenetic Relationships in the Genus Onoseris (Asteraceae, Mutisieae) Inferred from Morphology

Abstract Onoseris (Asteraceae, Mutisieae) is a genus of 31 species distributed from Mexico to Argentina through the Andes with its center of diversity in Peru. A phylogenetic analysis based on a detailed morphological study is provided. Urmenetea is used as the outgroup. Three most parsimonious cladograms are obtained based on the complete data set using Paup* 4.0b8. Two monophyletic groups are recognized: 1. Species with petiolate leaves, palmately veined blades with hastate base, and few-headed capitulescences, rarely thyrsoid capitulescences (O. acerifolia, O. alata, O. brasiliensis, O. cabrerae, O. castelnaeana, O. costaricensis, O. donnell-smithii, O. drakeana, O. fraterna, O. hastata, O. macbridei, O. onoseroides, O. peruviana, O. purpurea, O. sagittata, O. silvatica, and O. speciosa). 2. Species with sessile or subsessile leaves, elliptic and pinnately veined blades with attenuate base, and solitary capitula (O. albicans, O. amplexicaulis, O annua, O. chrysactinioides, O cumingii, O. gnaphalioides, O. humboldtiana, O. hyssopifolia, O. linearifolia, O. lopezii, O. minima, O. odorata, O. salicifolia, and O. weberbaueri). These monophyletic groups are recognized as subgenera Onoseris and Hipposeris respectively. Onoseris salicifolia is chosen as the lectotype of Onoseris subg. Hipposeris. Corolla polymorphism within Onoseris shows that corolla morphology alone cannot be used to distinguish between subtribes Mutisiinae and Gochnatiinae. Biogeographically, Onoseris has a continuous distribution from the Southern Andes to Northern Andes and Central America, but no individual species is distributed on both sides of the Huancabamba Zone. A group of species in subgenus Onoseris distributed in Central America and Brazil are regarded as phylogenetically derived (e.g., O. brasiliensis, O. costaricensis, O. onoseroides).