Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Approaches to Predict the Non-canonical DNAs

Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.
Evaluation and Treatment of Vascular Cognitive Impairment by Transcranial Magnetic Stimulation

The exact relationship between cognitive functioning, cortical excitability, and synaptic plasticity in dementia is not completely understood. Vascular cognitive impairment (VCI) is deemed to be the most common cognitive disorder in the elderly since it encompasses any degree of vascular-based cognitive decline. In different cognitive disorders, including VCI, transcranial magnetic stimulation (TMS) can be exploited as a noninvasive tool able to evaluate in vivo the cortical excitability, the propension to undergo neural plastic phenomena, and the underlying transmission pathways. Overall, TMS in VCI revealed enhanced cortical excitability and synaptic plasticity that seem to correlate with the disease process and progression. In some patients, such plasticity may be considered as an adaptive response to disease progression, thus allowing the preservation of motor programming and execution. Recent findings also point out the possibility to employ TMS to predict cognitive deterioration in the so-called “brains at risk” for dementia, which may be those patients who benefit more of disease-modifying drugs and rehabilitative or neuromodulatory approaches, such as those based on repetitive TMS (rTMS). Finally, TMS can be exploited to select the responders to specific drugs in the attempt to maximize the response and to restore maladaptive plasticity. While no single TMS index owns enough specificity, a panel of TMS-derived measures can support VCI diagnosis and identify early markers of progression into dementia. This work reviews all TMS and rTMS studies on VCI. The aim is to evaluate how cortical excitability, plasticity, and connectivity interact in the pathophysiology of the impairment and to provide a translational perspective towards novel treatments of these patients. Current pitfalls and limitations of both studies and techniques are also discussed, together with possible solutions and future research agenda.
Inhibition of nucleotide synthesis mediates replicative senescence of human mammary epithelial cells

Cellular senescence is a mechanism by which cells permanently withdraw from the cell cycle in response to stresses including telomere shortening, DNA damage, or oncogenic signaling. Senescent cells contribute to both age-related degenerative pathologies and hyperplastic pathologies including cancer. In culture, normal human epithelial cells enter senescence after a limited number of population doublings, known as replicative senescence. Here, to investigate how metabolic pathways regulate replicative senescence, we used liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to analyze senescent primary human mammary epithelial cells (HMEC). We did not observe significant changes in glucose uptake or lactate secretion in senescent HMEC. However, analysis of intracellular metabolite pool sizes demonstrated that senescent cells exhibited depletion of metabolites from nucleotide synthesis pathways. Furthermore, stable isotope tracing with 13C-labeled glucose and glutamine revealed a dramatic blockage of flux into nucleotide synthesis pathways in senescent HMEC. To test whether cellular immortalization would reverse these observations, we expressed telomerase in HMEC. In addition to preventing senescence, telomerase expression maintained metabolic flux from glucose into nucleotide synthesis pathways. Finally, we tested whether inhibition of nucleotide synthesis in proliferating HMEC was sufficient to induce senescence. Treatment of proliferating HMEC with an inhibitor of ribonucleotide reductase regulatory subunit (RRM2), a rate limiting enzyme in dNTP synthesis, induced premature senescence with concomitantly decreased metabolic flux from glucose into nucleotide synthesis. Taken together, our results suggest that inhibition of nucleotide synthesis plays a causative role in establishment of replicative senescence in HMEC.
A bivariate longitudinal model for psychometric data

Psychometric test data are useful for predicting a variety of important life outcomes and personality characteristics. The Cognitive Reflection Test (CRT) is a short, well-validated rationality test, designed to assess subjects’ ability to override intuitively appealing but incorrect responses to a series of mathand logic-based questions. The CRT is predictive of many other cognitive abilities and tendencies, such as verbal intelligence, numeracy, and religiosity. Cognitive psychologists and psychometricians are concerned with whether subjects improve their scores on the test with repeated exposure, as this may threaten the test’s predictive validity. This project uses the first publicly available longitudinal dataset derived from subjects who took the CRT multiple times over a predefined period. The dataset includes a multitude of predictors, including number of previous exposures to the test (our variable of primary interest). Also included are two response variables measured with each test exposure: CRT score and time taken to complete the CRT. These responses serve as a proxy for underlying latent variables, “rationality” and “reflectiveness”, respectively. We propose methods to describe the relationship between the responses and selected predictors. Specifically, we employ a bivariate longitudinal model to account for the presumed dependence between our two responses. Our model also allows for subpopulations (“clusters”) of individuals whose responses exhibit similar patterns. We estimate the parameters of our oneand two-cluster models via adaptive Gaussian quadrature. We also develop an Expectation-Maximization algorithm for estimating models with greater numbers of clusters. We use our fitted models to address a range of subject-specific questions in a formal way (building on earlier work relying on ad hoc methods). In particular, we find that test exposure has a greater estimated effect on test scores than previously reported and we find evidence of at least two subpopulations. Additionally, our work has generated numerous avenues for future investigation.
Comparing management schemes for forest certification and timber-legality verification: Complementary or competitive in indonesia?

ABSTRACT Indonesian small-scale forest holders are facing a dilemma due to the implementation of a mandatory national timber-legality verification scheme and an internationally popular forest certification scheme. The problems arise from limited financial, technical, and administrative information concerning the most preferred scheme and the “imperfection of such a scheme” for long-term business needs. Using the Forest Certification Assessment Guide (FCAG) this paper identifies the characteristics of four third-party forest certification schemes currently working in Indonesia, namely FSC, PEFC, LEI, and SVLK. An online questionnaire was used to survey a wide range of respondents about the future development of contested schemes and those preferred by small-scale forest holders. Our findings show that although FSC scheme obtained the highest score and is considered the best scheme according to the FCAG, small-scale forest holders prefer SVLK scheme, which had the lowest FCAG score because of its mandatory nature and available subsidies. Statements by the four schemes’ proponents, which delegitimize other schemes, reveal they are in competition especially in winning market acceptance and local adaptability. Finally, we suggest proponents enhance aspects where their schemes are lacking and contrive a comparable certification scheme in order to induce willingness to be certified.
Plutonium isotopic composition by gamma-ray spectroscopy

We discuss the general approach, computerized data analysis methods, and results of measurements to determine the isotopic composition of plutonium by gamma-ray spectroscopy. The simple techniques are designed to be applicable to samples of arbitrary size, geometry, chemical and isotopic composition that have attained /sup 241/Pu-/sup 237/U equilibrium. The combination of the gamma spectroscopic measurement of isotopic composition coupled with calorimetric measurement of total sample power is shown to give a totally nondestructive determination of sample Pu mass with a precision of 0.6% for 1000-g samples of PuO/sub 2/ with 12% /sup 240/Pu content. The precision of isotopic measurements depends upon many factors including sample size, sample geometry, and isotopic content. Typical ranges are found to be /sup 238/Pu, < 1 to 10%; /sup 239/Pu, 0.1 to 0.5%; /sup 240/Pu, 2 to 5%; /sup 241/Pu, 0.3 to 0.7%; /sup 242/Pu (determined by isotopic correlation); and /sup 241/Am, 0.2 to 10%.
Preparation, characterization and applications of functionalized carbon nano-onions

OF DISSERTATION PREPARATION, CHARACTERIZATION AND APPLICATIONS OF FUNCTIONALIZED CARBON NANO-ONIONS Carbon nano-onions (CNOs) discovered by Ugarte in 1992 are multi-layered fullerenes that are spherical analogs of multi-walled carbon nanotubes with diameters varying from 6 nm to 30 nm. Among the various methods of synthesis, CNOs prepared by graphitization of nanodiamonds (N-CNOs) and underwater electric arc of graphite rods (A-CNOs) are the subject of our research. N-CNOs are considered as more reactive than A-CNOs due to their smaller size, high curvature and surface defects. This dissertation focuses on structural analysis and surface functionalization of NCNOs with diameters ranging from 6—10 nm. Synthetic approaches such as oleumassisted oxidation, Freidel-Crafts acylation and Billups reductive alkylation were used to functionalize N-CNOs to improve their dispersion properties in aqueous and organic solvents. Functionalized N-CNOs were characterized using various techniques such as TGA, TG-MS, Raman spectroscopy and pH-titrimetry. We designed an experimental method to isolate polycyclic aromatic adsorbates formed on the surface of oleum oxidized N-CNOs (ON-CNOs) and characterized them. A-CNOs, on the other hand are bigger than N-CNOs with diameters ranging from 20—40 nm. In this dissertation, we discuss the preparation of graphene structures by unzipping of A-CNOs using KMnO4 as oxidizing agent. These graphene structures were characterized using powder X-ray diffraction, TGA, BET nitrogen adsorption/desorption studies and compressed powder conductivity. This dissertation also focuses on lithiation/delithiation studies of N-CNOs, ACNOs and A-CNO-derived graphene structures to use them as negative electrode materials in lithium-ion batteries. The cycling performances of these materials at a charge/discharge rate of C/10 were discussed. The cycling performance of N-CNOs was tested at faster charge/discharge rate of C.
Common Sense Reasoning in Autonomous Artificial Intelligent Agents Through Mobile Computing

This thesis presents the design, analysis, and implementation of an autonomous artificial intelligent agent capable of planning, reasoning, rationalizing, communication, and learning through the use of common-sense reasoning. We discuss the cognitive modeling approach of our autonomous artificial intelligent agent and how its system design is inspired by biological inspired cognitive processes of the human brain (Crowder, 2012; Mallot et al., 2009; Trullier et al., 1997; Goertzel et al., 2010). We cover how our autonomous intelligent agent utilizes stacked artificial neural networks, combined classifiers, memories, and fuzzy systems to map out its cognitive process through unsupervised and semi-supervised learning. We state our motivations for performing this research and examine the importance of common-sense reasoning in the advancements of artificial intelligence. We cover various roles and applications of autonomous artificial intelligent agents as well as the challenges that arise when developing intelligent agents that can perceive, learn, and adapt autonomously. The outcome of this thesis includes the development of a mobile software application comprising an autonomous artificial intelligent agent that demonstrates an understanding of context, observations, utilization of past experiences, self-improvement through reinforcement learning, and hypothesis development to reach solutions – which are presented and illustrated with examples and
Zehneria grandibracteata (Cucurbitaceae), an overlooked new species from western Kenyan forests

Abstract Zehneria grandibracteata, a new species of Cucurbitaceae from western Kenya, is described here, based on morphological and molecular data. It has long been misidentified as the widely-distributed species Z. scabra. However, it differs by its ovate leafy probract at the base of the inflorescences, subglabrous condition of the entire plant, shorter receptacle-tube and filaments, as well as denser and sessile inflorescences. Furthermore, the molecular phylogenetic analysis of Zehneria, based on nrITS sequences, further supports the argument that Z. grandibracteata should be segregated from Z. scabra.
Comparative Analysis of Haematological Parameters in Hookworm and Plasmodium falciparum Co-Infected Individuals in Kintampo North Municipality, Ghana

Background: Hookworm and Plasmodium falciparum are endemic in Ghana, especially in the north-east and middle belt areas. Haematological parameters have been shown to predict the presence of these infections in patients. This study investigated the effect of hookworm-P. falciparum co-infection on haematological parameters among the patients. Methodology: Stool and blood samples from 984 participants in a cross-sectional study conducted in the Kintampo North Municipality of Ghana were examined for hookworm and Plasmodium falciparum parasites. Malaria parasitaemia was estimated by microscopy and Plasmodium falciparum-specific 18S rRNA gene by polymerase chain reaction. Hookworm eggs in faecal samples were analyzed using Kato-Katz and formol-ether concentration methods. Hookworm speciation was done by PCR. Estimation of haematological parameters was done by automated haematology analyzer. Tukey multiple comparisons test was used to compare continuous variables among the infected groups and Spearman’s rank correlation test determined the relationships between variables. Results: The overall mean (SD) age of the study participants was 22.8 (17.4). Mean lymphocytes and eosinophils counts were higher while mean neutrophil and monocytes counts were lower in the co-infected individuals compared to the single infections. The mean red blood cell (RBC) count and haemoglobin (Hb) levels were higher in the co-infected individuals than in those with malaria only infection. However, white blood cell count and platelet counts were not statistically significant among the groups. There was a significant negative correlation between malaria parasite density and Hb level (r = - 0.239, p = 0.001) Conclusion: Hookworm and Plasmodium falciparum co-infections showed an increased in lymphocyte, eosinophil count and Haemoglobin levels, but a decrease in neutrophil and monocyte levels compared to malaria only infection. The possible mechanisms accounting for the variations in haematological levels remain to be elucidated.
The Distribution And Average Size Of Granular Gland In Poisonous Rock Frog, Odorrana hosii

Frog skin is reported to have potential in medical application especially the granular gland on the skin producing secretion containing peptide. The objective of this paper was to examine the distribution and average size of granular glands in Odorrana hosii’s skin. The skin histology was stained with Haematoxylin-Eosin to identify granular gland. Results revealed that the distributions of granular glands were statistically significantly different between six regions of the frog skin (F (5,234) =3.47, p=0.005) with dorsal central region of skin has the highest mean number of granular gland (2.22 ± 1.69). The average size of the granular glands was statistically significantly different between six skin regions (F (5,234)=4.04, p=0.012) with dorsal central region contained the biggest granular gland size (11.95 x 103 μm2). This study showed that the granular glands in O. hosii were significantly abundant in dorsal head region and the largest size was in the dorsal central region as compared to other regions of the skin. This implicates the dorsal head and central skin region can be used for peptides extraction due to the abundance and size of granular glands.
Getting Physically Active by E-Bike: An Active Commuting Intervention Study

Introduction: Increased physical activity (PA) is a major component in promoting public health, and active commuting could make an important contribution. Using an electric bicycle (e-bike) is reported to be of at least moderate intensity PA and is an alternative to other modes of transport for commuting. We aimed to explore the experience of commuting by e-bike in an intervention study. Methods: Focus group interviews with 21 previously inactive participants from three cities in Norway, who were given access to an e-bike for commuting for three (N = 2) or eight months (N = 19). Participants cycled for 226 days on average. The interviews were analyzed using systematic text condensation. Results: The use of e-bikes and active commuting stimulated some participants to take on additional PA in their leisure time. Others preferred active commuting to be their daily PA. Participants’ experiences of commuting by e-bike were characterized by a motivational shift from external reasons for e-biking, such as pressure to get fit, to feelings of well-being, enjoyment and recognition of the health benefits. Conclusion: Commuting by e-bike was convenient and promoted good health. Promoting e-bikes could lead to long term changes among inactive people because positive experiences stimulate autonomous reasons for active commuting.
REMOVAL OF FLUORIDE IONS BY ION EXCHANGE RESIN: KINETIC AND EQUILIBRIUM STUDIES

The extent of the problem of the excessive fluoride in drinking water remains an important health issue. In the present work, strong-base anion resins were investigated to assess their sorptive removal capacity of fluoride from water. It was found that the removal of fluoride was high at natural pH (7) and was improved for increasing contact time and adsorbent dosage. The maximum sorption of the resin was 13.7 mg/g according to the Langmuir model, namely higher than the values reported in the literature for other sorbents and in the range of maximum capacities of some geo-materials, showing the efficiency of strong-base anion resins for fluoride removal. Among the Langmuir, Freundlich and Temkin isotherm models tested, it was found that the Freundlich model was the most appropriate to describe fluoride sorption at equilibrium (r2>0.99); while among the pseudo-first order, pseudo-second order and modified pseudo-first order models, the pseudo-first order model was found to match experimental kinetic data. It was also shown that the rate-limiting step was the film diffusion rather than the intra-particle diffusion. A simple and efficient statistical method, based on factorial design analysis using linear regression model, was applied for the determination of the optimal removal conditions deduced from 3D plots and contour plots. To approach real conditions, the effect of co-existing ions showed slightly reverse effect of hardness and chloride ions while a higher reverse effect for nitrate. Contrarily, sulfate had no significant effect on fluoride removal.
Solution Processed Semiconductor Nanostructures and Nanocomposites for Dye Sensitized Solar Cells

ZnO nanorods have been studied extensively due to facile synthesis and useful optoelectronic properties for applications in nanoscale devices. In a common two-step procedure, an ethanolic Zn 2+ precursor solution is used to deposit ZnO seed crystals on a substrate, which is then immersed in an aqueous Zn 2+ precursor solution to grow the nanorods. Here, a forced hydrolysis technique was employed based on additions of water and heat to the seed precursor solution before depositing the seeds on commercial FTO/glass substrates. ZnO nanorods were then grown from these seeds by chemical bath deposition. Analyses showed that the forced hydrolysis resulted in an increase in seed crystallite size and a decrease in the number of seeds deposited. With increasing seed size, the number density of nanorods decreased, while the length and diameter of each rod increased. These findings offer a simple method for exerting control over the number density of ZnO nanorods that is compatible with the rough FTO surface, unlike other methods that require smoother substrates.
A novel mode of interaction between intrinsically disordered proteins

An increasing number of proteins, which have neither regular secondary nor well-defined tertiary structures, have been found to be present in cells. The structure of these proteins is highly flexible and disordered under physiological (native) conditions, and they are called “intrinsically disordered” proteins (IDPs). Many of the IDPs are involved in interactions with other biomolecules such as DNA, RNA, carbohydrates, and proteins. While these IDPs are largely unstructured by themselves, marked conformational changes often occur upon binding to an interacting partner, which is known as the “coupled folding and binding mechanism”, which enable them to change the conformation to become compatible with the shape of the multiple target biomolecules. We have studied the structure and interaction of eukaryotic transcription factors Sp1 and TAF4, and found that both of them have long intrinsically disordered regions (IDRs). One of the IDRs in Sp1 exhibited homo-oligomer formation. In addition, the same region was used for the interaction with another IDR found in the TAF4 molecule. In both cases, we have not detected any significant conformational change in that region, suggesting a prominent and novel binding mode for IDPs/IDRs, which are not categorized by the well-accepted concept of the coupled folding and binding mechanism.