Miracle-dz/UniFAR-FTUs huggingface dataset:
Rigid-body Motion and Pagerank Matrix Computations and Applications

• The submission should consist of: – The complete report, including * A front page with the following information: 1. Your name. 2. The course name. 3. Your username at the Department of Computing Science. 4. The assignment number. 5. The version of the submission (in case of re-submissions). – An appendix with the source code. – To simplify feedback, the main report (optionally excluding the appendix) must have numbered sections and page numbers. Furthermore, all equations should be numbered, even if they are not referred to in the text. • The submitted code must be Matlab-compatible. If you choose to work in Octave, verify that your code is Matlab-compatible before you submit your assignment. • If you write your report using L A T E X, double-check that your references are ok and not " Figure ? " before you submit. • Furthermore, the source code should be available in a folder called edu/5da002/assN in your home folder, where N is the assignment number. You will probably have to create the folder yourself.
My scientific life

I was born in Canero, Spain, a very small village in the north coast of Asturias. When I was one year old, my parents moved to Gij on, also in Asturias, where I spent my childhood and early youth. There, I attended the school and obtained the baccalaureate title in 1954. Since I wanted to pursue a university career, I had to spend one year doing the so-called pre-university studies and to decide whether I wanted to follow a scientific or a humanistic career. I choose to go into science. At the end of the year I had to decide which specific career I wanted to follow. I doubted between medicine and chemistry. Since medicine was not available at Oviedo University, close to Gij on, I decided to go to Madrid University to follow a course common for both careers. Finally, I decided to study chemistry. In the third year we studied organic chemistry, and I enjoyed very much the long hours we spent in the laboratory. I thought that, in the future, I would like to do research in organic chemistry. But that was not the case. In the summer of 1958, when I had finished my third year of chemistry, I went to Gij on to spend the holidays, and I was very lucky to meet Severo Ochoa, which had a decisive influence on my future. I attended a conference he gave about his work and I was fascinated by his talk. Since my father was a good friend of Ochoa, besides being cousins in law, I had the chance to talk to him about my future. I had not yet studied biochemistry and he promised to send me a biochemistry book. I was very excited when I received the book General Biochemistry by Fruton and Simmonds, dedicated by Severo Ochoa. When I finished my chemistry studies I had decided to dedicate myself to biochemistry. Ochoa advised me to do the Ph.D. Thesis in Madrid with Alberto Sols, an excellent biochemist, who had been trained with Carl and Gerty Cori at the Washington University School of Medicine in St. Louis. Then, I could go to Ochoa’s laboratory at New York University (NYU) School of Medicine for a postdoctoral training. Ochoa wrote me a reference letter for Alberto Sols who accepted me, even if I was a woman, since he could not refuse a request made by Severo Ochoa who had already obtained the Nobel Prize. Thus, in January 1961, I started my Ph.D. Thesis working on carbohydrate metabolism, mainly on glucose-phosphate isomerase from yeast. I found that the enzyme has an anomerase-like activity producing the open form of glucose6-phosphate. This was the first finding in my scientific career, something that was very exciting for me. The work was published in the Journal of Biological Chemistry. At the end of my studies in chemistry, I
Marine Microbiology: Challenges and Future Directions

The planet earth is believed to have formed about 4600 million years ago and life forms originated at about 3,500 million years on this planet. As we know Antonie van Leeuwenhoek (1632-1723) was the first to observe bacteria (he called them as “animalcules”) under a microscope he invented. He might have thought that scientists who would follow him would discover many more such microscopic organisms from different niches. His dream came true but at a pace, which he would not have thought about. With the introduction of better microscopy, our ability to observe natural samples improved tremendously and we started recognizing the ubiquitous nature of the tiny creatures of the planet earth. However, the introduction of modern molecular techniques in late seventies revolutionized our understanding of these organisms, especially the microorganisms. Now we know that these microbes are present everywhere from the permanently frozen continents, high altitudes (up to 60 km high in the atmosphere), thermal springs, deepseas to even deep-sea hydrothermal vents. They are the building blocks of any ecosystem and perform varied and all-important tasks that include everything from pathogenesis to fixing atmospheric nitrogen in the soil. An interesting question to be asked, therefore, is: has there been any realistic estimate of these bacteria on Earth? Now, for the first time, a team of researchers from the University of Georgia (USA) led by microbiologist William B.Whitman (1998), has come up with direct estimate of the total number of bacteria on earth. They estimate the number to be five million trillion trillion – i.e., a five with 30 zeroes after it. They also give a picturization of these numbers: If each bacterium is a penny, and when stacked flat one over the other, the stack would reach a trillion light years. These almost incomprehensible numbers give only a sketch of the vast pervasiveness of microbes in general and bacteria in particular, in their natural world.
Diamond for Fiber-Optic Raman Spectroscopy

DIAMOND FOR QUANTITATIVE FIBER OPTIC RAMAN SPECTROSCOPY Jianli Zheng Old Dominion University, 1997 Director: Dr. Sacharia Albin Raman spectroscopy is a powerful technique for molecular structural studies and concentration measurement. Being a single beam technique, the Raman intensity depends on the optical power of the excitation source, optical alignment of the system, detector response as well as species concentration. To eliminate the unwanted variations in the system and get the concentration information of the species, intensity referencing is necessary. The existing referencing methods either use a constant Raman band of the sample, or add a chemically inert material with known concentration into the sample. Unfortunately, the former method is not always applicable and the latter is not acceptable for in situ process monitoring. A new concept of using diamond as an intensity standard in quantitative Raman analysis is presented in this dissertation. Combined with fiber optics, a self-referenced universal Raman probe is developed. Performances of five probe designs are investigated. Results indicate that diamond-referenced probes are insensitive to the excitation power fluctuation and optical alignment. Chemical vapor deposited (CVD) diamond film is investigated as an alternative to the expensive bulk diamond. The CVD diamond referenced probe shows performance similar to the bulk diamond probe. A remote measurement is also performed with a 500-foot fiber probe, which shows the potential of long distance in situ concentration monitoring in an industrial environment. R eproduced with perm ission of the copyright owner. Further reproduction prohibited without perm ission.
Integrating code smells detection with refactoring tool support

Refactoring is a form of program transformation which preserves the semantics of the program. Refactoring frameworks for object-oriented programs were first introduced in 1992 by William Opdyke. Few people apply refactoring in mainstream software development because it is time consuming and error-prone if done by hand. Since then, many refactoring tools have been developed but most of them do not have the capability of analyzing the program code and suggesting which and where refactorings should be applied. Previous work discusses many ways to detect refactoring candidates but such approaches are applied to a separate module. This work proposes an approach to integrate a "code smells'' detector with a refactoring tool. To the best of our knowledge, no work has established connections between refactoring and finding code smells in terms of program analysis. This work identifies some common analyses required in these two processes. Determining which analyses are used in common allows us to reuse analysis information and avoid unnecessary recomputation which makes the approach more efficient. However, some code smells cannot be detected by using program analysis alone. In such cases, software metrics are adopted to help identify code smells. This work also introduces a novel metric for detecting "feature envy''. It demonstrates that program analysis and software metrics can work well together. A tool for Java programs called JCodeCanine has been developed using the discussed approach. JCodeCanine detects code smells within a program and proposes a list of refactorings that would help improve the internal software qualities. The programmer has an option whether to apply the suggested refactorings through a "quick fix''. It supports the complete process allowing the programmer to maintain the structure of his software system as it evolves over time. Our results show that restructuring the program while trying to preserve its behavior is feasible but is not easy to achieve without programmer's declared design intents. Code smells, in general, are hard to detect and false positives could be generated in our approach. Hence, every detected smell must be reviewed by the programmer. This finding confirms that the tool should not be completely automated. An semi-automated tool is best suited for this purpose.
DTI and MTI parameters correlate in periventricular white matter hyperintensities in old age

M. E. Bastin, J. D. Clayden, A. Pattie, I. F. Gerrish, J. M. Wardlaw, and I. J. Deary Medical Physics, University of Edinburgh, Edinburgh, Mid Lothian, United Kingdom, Neuroinformatics, University of Edinburgh, Edinburgh, Mid Lothian, United Kingdom, Psychology, University of Edinburgh, Edinburgh, Mid Lothian, United Kingdom, Clinical Neurosciences, University of Edinburgh, Edinburgh, Mid Lothian, United Kingdom
Discrete Entropy

3 Information Theory 15 3.1 Secure Encryption . 15 3.2 Data Compression . 17 3.2. 1 Uniquely Decodable and Prefix-free Codes . 17 3.2. 2 Huffman Codes . 20 3.3 Guessing From Partial Information . 21 3.4 Shannon’s Channel Coding Theorem . 22
Patterns of Cross-Reactivity in Patients with Immediate Hypersensitivity Reactions to Gadobrutol.

quality of life questionnaire in yellow jacket allergic patients. J Allergy Clin Immunol. 2002;109:162-7. 3. Armisen M, Guspi R, Alfaya T, Cruz S, Fernández S, DomínguezNoche C, et al. Cross-sectional validation of a quality of life questionnaire in Spanish for patients allergic to hymenoptera venom. J Invest Allegol Clin Immunol. 2015;25(3):176-82. 4. Alfaya T, Vega A, Domínguez-Noche C, Ruiz B, Marqués L, Sánchez-Morillas L. Longitudinal validation of the Spanish Version of the Health-Related Quality of Life Questionnaire for Hymenoptera Venom Allergy (HRQLHA). J Invest Allergol Clin Immunol. 2015;25(6):426-30. 5. Sturm GJ, Varga EM, Roberts G, Mosbech H, Bilo MB, Akdis CA, et al. EAACI guidelines on allergen immunotherapy: Hymenoptera venom allergy. Allergy. 2018;73(4):744-64. 6. Biló MB, Bonifazi F. The natural history and epidemiology of insect venom allergy: clinical implications. Clin Exp Allergy. 2009;39:1467-76. 7. Tripolt P, Arzt-Gradwohl LA, Cerpes U, Laipold K, Binder B, Sturm GJ. Large local reactions and systemic reactions to insect stings: similarities and differences. PLoS One. 2020;15(4). e0231747. 8. Bilo MB, Pravettoni V, Bignardi D, Bonadonna P, Mauro M, Novembre E, et al. Hymenoptera venom allergy: management of children and adults in clinical practice. J Invest Allergol Clin Immunol. 2019;29(3):180-205. 9. Golden DB, Kelly D, Hamilton RG, Craig TJ. Venom immunotherapy reduces large local reactions to insect stings. J Allergy Clin Immunol. 2009;123:1386-90. 10. Severino MG, Cortellini G, Bonnadonna P, Francescato E, Panzini L, Macchia D, et al. Sublingual immunotherapy for large local reactions caused by honeybee sting: a double-blind placebo-controlled trial. J Allergy Clin Immunol. 2008;122:448.
A Method for Mining Granger Causality Relationship on Atmospheric Visibility

Atmospheric visibility is an indicator of atmospheric transparency and its range directly reflects the quality of the atmospheric environment. With the acceleration of industrialization and urbanization, the natural environment has suffered some damages. In recent decades, the level of atmospheric visibility shows an overall downward trend. A decrease in atmospheric visibility will lead to a higher frequency of haze, which will seriously affect people's normal life, and also have a significant negative economic impact. The causal relationship mining of atmospheric visibility can reveal the potential relation between visibility and other influencing factors, which is very important in environmental management, air pollution control and haze control. However, causality mining based on statistical methods and traditional machine learning techniques usually achieve qualitative results that are hard to measure the degree of causality accurately. This article proposed the seq2seq-LSTM Granger causality analysis method for mining the causality relationship between atmospheric visibility and its influencing factors. In the experimental part, by comparing with methods such as linear regression, random forest, gradient boosting decision tree, light gradient boosting machine, and extreme gradient boosting, it turns out that the visibility prediction accuracy based on the seq2seq-LSTM model is about 10% higher than traditional machine learning methods. Therefore, the causal relationship mining based on this method can deeply reveal the implicit relationship between them and provide theoretical support for air pollution control.
Metabolic Understanding of the Genetic Dysregulation in the Tumor Microenvironment of Kidney Renal Clear Cell Carcinoma

The metabolic dysregulation is a hallmark of cancers including KIRC, specifically caused by alterations in metabolic genes. Currently, a lack of consensus exists between metabolic signatures in the tumor microenvironment. Here, in this study, we observed the significant correlations of differentially expressed metabolic genes (DEmGs) between KIRC and the related normal samples. Briefly, we collected sets of metabolic genes through RNA-seq data of KIRC and normal tissues from TCGA, followed by the identification of KIRC-related DEmGs. Next, patients were classified into three clusters, and using WGCNA, we identified metabolic genes involved in the survival among different clusters. Furthermore, we investigated survival and clinical parameters along with immune infiltration in the clusters. At the same time, we constructed and validated a prediction model based on these DEmGs. These analyses revealed that the patients having high expression of DEmGs showed poor survival, while infiltration of less-immune cells was associated with the metastasis of KIRC. In the end, we identified NUDT1 as a hub gene as it showed significantly high expression in KIRC samples as well as associated with the survival and prognosis of the patients. Further analysis revealed the oncogenic role of NUDT1 in 786-O and ACHN cells. Thus, we conclude that NUDT1 could be a potential diagnostic and prognostic marker for KIRC.
Psychosocial Predictors of Body Weight Congruence in Adolescents Aged 15 and 17 Years in Poland: Findings from the Health Behaviour in School-Aged Children (HBSC) Study

Background: Body weight congruence (BWC) has implications for adolescent health. The main goal of this study was to examine the distribution of BWC and its relationship with six psychosocial factors. Methods: A representative sample of N = 3508 adolescents aged 15 and 17 years (52.4% girls) derived from the Health Behaviour in School-aged Children study, conducted in 2017/2018 in Poland, was used. BWC groups were defined based on self-reported BMI and subjective assessment of weight: (1) correct perception; (2) overestimation, and (3). underestimation. Principal component analysis (PCA) extracted the following two factors: a socio-relational factor (SR) related to perceived social support and social self-efficacy, and a body attitudes and social media exposure factor (BAME). Using the total sample, multinomial logistic regression was applied to estimate their impact on the BWC, and gender-specific models were compared. Results: Half (48.6%) of the adolescents correctly estimated their body weight, 31.0% overestimated it (girls 43.9%, boys 17.1%), and 20.0% underestimated it (boys 37.2%, girls 9.0%). Overestimation of body weight concerns 48.0% of normal weight girls, 50.0% of underweight girls, and 21.3% and 32.1% of normal weight and underweight boys, respectively. The percentage of normal weight (34.4%), and overweight and obese (30.8%) boys who underestimated their body weight was three times higher than the respective percentages of girls that underestimated their weight (9.0% and 11.9%). The SR factor protected adolescents from both underestimation (only in girls) and overestimation in the total sample (OR 0.74, 95%CI 0.68–0.81) and both genders. BAME increased this risk of overestimation in both genders (OR = 1.83, 95%CI 1.67–2.0), and the risk of underestimation among boys. Conclusions: Prevention programmes should include a wide range of psychosocial factors to improve BWC among adolescents.
Programming in Martin-Löf's Type Theory

data type, 179 abstraction, 14 Abstraction rule, 143 absurdity, 43 append, 68 application, 13 Application rule, 143 apply, 48, 148 arity of an expression, 18 Assumption rule, 123, 142 AUTOMATH, 8 axiom of choice, 115 Bishop, 6 Bool, 44 Bool rules, 44–45 Boolean, 44–45 Calculus of Constructions, 8 canonical expression, 26 cartesian product of a family of sets, 47–55, 148 case{i1,. ,in}, 41 case, 151 Church, 17 combination, 15 combined expression, 17 conjunction, 74 cons, 67, 152 Constable, 6, 167 constructive mathematics, 6 context, 29, 139 Coquand, 3, 7, 8 Curry, 10 Curry-Howard interpretation, 6 Cut rule for elements in sets, 124 Cut rule for equal elements in sets, 124 Cut rule for equal sets, 123 Cut rule for propositions, 123 Cut rule for true propositions, 124 de Bruijn, 8, 10 definiendum, 19 definiens, 19 definitional equality of expressions, 15 Dijkstra, 167, 171 disjoint union of a family of sets, 81– 82, 149 disjoint union of two sets, 79–80, 150 Dummet, 6 El formation rule, 139 elimination rule, 35 empty set, 43 enumeration sets, 41–42, 151 Eq, 57 Eq rules, 60–61 equality as a proposition, 57, 117 between canonical elements, 27 between elements in a set, 29, 31, 37, 119, 121 between expressions, 15 between sets, 28, 30, 37, 118, 121 extensional, 57 identity between objects in a type, 138 identity between types, 138 intensional, 57 equality rule, 35 equality sets, 57–62, 150 examples: Bool has only the elements true and false, 161 A partitioning problem, 171 Decidable predicates, 162 Division by 2, 155 Even or odd, 159 Module for sets with a computable equality, 182 Stack of A elements, 182 Stack of natural numbers, 179 Stronger elimination rules, 163 existential quantifier, 81, 82 expressions, 13 arity, 18 canonical —, 26 combined —, 17 saturated —, 17 single —, 17 unsaturated —, 17 extensional equality, 57 wfalse, 44 Fermat’s last theorem, 4 formation rule, 35 Frege, 17
The Application of the Best-Worst Method to Gain the Premier Modified Asphalt Mixtures

The main purpose of Hot Mix Asphalt (HMA) is to choose the most suitable and the most affordable mix of bitumen and aggregates, so that it can maintain the technical properties of the asphalt concrete in certain amounts. Different methods have been suggested for mixing the Hot Mix Asphalt (HMA) including the Marshall method, the modified Marshall method, Hveem method, and the Superpave mixing method. Concurrently, the project of mixing Hot Mix Asphalt (HMA) in Iran is done based on the Marshall method and the modified Marshall method. Regarding the weaknesses of the asphalt mixes in different situations, the engineers try to modify and improve the properties of the asphalt mix by use of different additives. On the other hand, the additional expenses of various additives to the asphalt mix for building one kilometer of the road is a negative parameter. However, by use of the additives, the technical properties of the asphalt mix improve. Therefore, to decide on a proper choice out of the alternatives would be a difficult task. This paper, tries to provide an appropriate method for evaluating and choosing the best alternative by taking into consideration all the technical criteria. In this article, we first evaluate the score and the weight of each alternative in each criterion. Then, the weight of each criterion is evaluated using the best-worst method, and eventually, taking all aspects into consideration, the rankings of different alternatives will be determined based on two situations: certain situation and uncertain situation.
Anomalous salting-out, self-association and pKa effects in the practically-insoluble bromothymol blue

Background and Purpose The widely-used and practically insoluble diprotic acidic dye, bromothymol blue (BTB), is a neutral molecule in strongly acidic aqueous solutions. The Schill (1964) extensive solubility-pH measurement of bromothymol blue in 0.1 and 1.0 M NaCl solutions, with pH adjusted with HCl from 0.0 to 5.4, featured several unusual findings. The data suggest that the difference in solubility of the neutral-form molecule in 1M NaCl is more than 0.7 log unit lower than the solubility in pure water. This could be considered as uncharacteristically high for a salting-out effect. Also, the study reported two apparent values of pKa1, 1.48 and 1.00, in 0.1 M and 1.0 M NaCl solutions, respectively. The only other measured value found for pKa1 in the literature is -0.66 (Gupta and Cadwallader, 1968). Experimental Approach It was reasoned that the there can be only a single pKa1 for BTB. Also, it was hypothesized that salting-out alone might not account for such a large difference in solubility observed at the two levels of salt. A generalized mass action approach incorporating activity corrections for charged species using the Stokes-Robinson hydration equation and for neutral species using the Setschenow equation, was selected to analyze the Schill solubility-pH data to seek a rationalization of these unusual results. Key Results BTB reveals complex speciation chemistry in saturated aqueous solutions which had been poorly understood for many years. The appearance of two different values of pKa1 at different levels of NaCl and the anomalously high value of the empirical salting-out constant could be rationalized to normal values by invoking the formation of a very stable neutral dimer (log K2 = 10.0 ± 0.1 M-1). A ‘normal’ salting-out constant, 0.25 M-1 was then derived. It was also possible to estimate the ‘self-interaction’ constant. The data analysis in the present study critically depended on the pKa1 = -0.66 reported by Gupta and Cadwallader. Conclusion A more reasonable salting-out constant and a consistent single value for pKa1 have been determined by considering a self-interacting (aggregation) model involving an uncharged form of the molecule, which is likely a zwitterion, as suggested by literature spectrophotometric studies.