Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphate interactions with proteins

﻿ Proton nuclear magnetic resonance (NMR) spectroscopy has been used to investigate the interaction of yeast phosphoglycerate kinase (PGK) with its phosphate containing substrates, ATP and 3-phosphoglycerate (3-PG). The application of one-dimensional and, for the first time, two-dimensional proton NMR techniques to this large protein has enabled specific resonance assignments to be made. Assignment has been aided by the investigation of specifically deuterated protein and site-specific mutant forms of the protein, including the isolated N- and C-domains. The effects of ATP and 3-PG binding on the proton NMR spectrum of yeast PGK have been characterised and the assigned resonances used as local probes of structural and dynamic changes. Two binding sites have been determined for the nucleotide substrate, ATP, the occupancies of which are dependent on Mg 2+ concentration. One site corresponds to the catalytic site determined crystallographically. A single binding site was found for 3-PG. This binding was shown to cause highly specific conformational changes throughout the N-domain and the interdomain region, which involve the relative movement of at least three α-helices. Investigation of 3-PG binding to several site-specific mutant forms of yeast PGK revealed a critical role for arginine 168 in the propagation of these changes. The general binding of anions to yeast PGK was investigated using the paramagnetic probes [Cr(CN) 6 ] 3- and [Fe(CN) 6 ] 3- , and the diamagnetic anion [Co(CN) 6 ] 3- . The primary anion binding site was determined from [Cr(CN) 6 ] 3- broadening data and found to share some side-chains involved in 3-PG binding, namely histidine 62 and arginine 168. Evidence for a secondary anion site was found. The anion binding data is discussed in view of the complex activation/inhibition effects of anions on the catalytic activity. Investigation of the isolated N- and C-domains showed that both can fold independently and confirmed that the C-domain is a nucleotide binding domain. It appears that the presence of the interdomain residues and/or the C-terminal peptide are necessary for 3-PG binding to the N-domain. This work shows that the specificity of the substrates is in binding, as expected, but also in the motions induced in the protein as a whole.
Evaluation of a Scoring System for predicting the risk of malignancy in thyroid nodules using Clinical, Laboratory and Sonological data

INTRODUCTION: Many patients present to the surgical department with a thyroid nodule. However not all require surgery and only 5-6% of these are malignant. There are many methods to diagnose and predict malignancy in thyroid nodules. This study throws light on the usefulness of combining clinical, radiological and laboratory investigations into a single scoring system which is used to predict the risk of malignancy in thyroid nodules thereby helping the surgeon to make appropriate decisions regarding the operative management and follow up of the patient. AIMS AND OBJECTIVES: To evaluate a scoring system using clinical, laboratory and sonological data for predicting the risk of malignancy in patients with thyroid nodules, in a tertiary care centre in South India, which caters mostly for an economically underprivileged population. MATERIALS AND METHODS: This prospective observational study involved 50 patients admitted in MMC, Chennai with thyroid nodules. Analysis of a scoring system was done which combined clinical findings, radiological features and laboratory findings such as TSH level and FNAC report. The final scores were compared with the post-operative histopathology of the patient and the risk of malignancy was predicted. OBSERVATION AND RESULTS: The scoring system had a maximum score of 26. The observed score ranged from 3 to 19. The mean score was 11. All the malignant cases observed in our study had a score greater than 11. The incidence of thyroid carcinoma for scores of 1 to 11 was 0%, 12 to 13 was 20%, 14 to 18 was 75% and ≥19 was 100%. The average risk of malignancy for a score ≤11 was 0% and for a score >11 was 54.166%. The sensitivity and specificity of the scoring system was 70.2% and 100% respectively. The positive and negative predictive value for the scoring system was 100% and 43.83% respectively.The greater risk of malignancy demonstrated for patients above a score of 11 was statistically significant (p < 0.0001, χ2 = 14.965, df = 1). The risk of malignancy increased with increasing scores and was found to be 100% for a score ≥16. CONCLUSION: This scoring system has proved to be accurate in predicting the risk of malignancy in patients with thyroid nodules by combining various parameters derived from the patient’s history, clinical examination and simple, cost-effective investigations like thyroid function test, ultrasonogram and FNAC. Each of these factors has variable reliability, but their combination has proven to be a better predictor of malignancy. It can be routinely introduced in every hospital for pre-operative assessment of patients presenting with thyroid nodules, thus helping the surgeon to make rational and individualized decision while treating such patients.
Male Zebra Finches and Bengalese Finches Emit Directed Songs to the Video Images of Conspecific Females Projected onto a TFT Display

Abstract In behavioral investigations examining mechanisms and functions of inter- and intra specific communications, whether one can manipulate stimulus properties is a critical factor. If we can substitute a real animal with an artificial model, that should greatly advance the research. Here we tested whether male zebra finches (Taeniopygia guttata castanotis) and male Bengalese finches (Lonchura striata var. domestica) emit natural behavior of directed singing to video images of conspecific females. When a conventional cathode ray tube (CRT) monitor was used, birds showed few signs of behavioral responses. However, when a thin film transistor (TFT) liquid crystal display was used, several behavioral responses, mostly sexual displays, to the images were observed. The amount of directed singing emitted towards the TFT projected images were comparable to that emitted to the live female birds in both species of birds. The reason why TFT monitor is much more powerful than CRT monitor in eliciting natural behavior from these birds may lie in the fact that TFT monitor is flickerless while CRT monitor might produce some flickers to the eye of birds that has high critical flicker frequency. TFT monitors should be better substitute of real objects than CRT monitors in behavioral investigations. This technique, combined with modern image processing techniques, should be useful for neuroethological studies of bird behavior.
Switching control for post-harvest food storage

Abstract: Harvested products inside a storage room are kept cool by a fan that blows air through a heat exchanger. The air and product temperature are regulated by switching the fan on and off. The corresponding mathematical model is nonlinear and discontinuous due to the switching of the fan. For control design, the model is approximated with a linear continuous model that has the switching time as input. For the approximated model, a controller that adjusts the switching time on every discrete time interval, is designed by classical design rules and tested on the original model by simulation.
Traditional post-harvest technology of cassava in Uganda.

Etude des methodes traditionnelles de conservation et de preparation du manioc, dans 4 regions d'Ouganda. Le but principal de l'etude est de tester l'efficacite des differentes methodes sur la teneur en acide cyanhydrique et en nutriment dans le manioc
Clarification of the Mating Procedure of Peucetia Viridans (Araneida: Oxyopidae) by a Microscopic Examination of the Epigynal Plug

In a study of the mating behavior of Peucetia viridans (Hentz), Whitcomb and Eason (1965) stated that the right palpus appeared to inseminate the left side of the epigynum, and the left palpus the right side. As their observations were inconclusive, and since the philosophical implications of such a possibility are important, we have investigated morphological evidence from which we conclude that the right palpus is used for the right side and vice versa. The male and female meet venter to venter, facing in the same direction (Whitcomb and Eason 1965), so that the left palpus is in line with the right side of the epigynum. No crossing over of the palpi was observed. Copulation is so rapid in this species and the palpi are alternated so quickly, however, that Whitcomb and Eason could not be certain that the palpi did not cross over. Observations of former workers, summarized by Gertsch (1949, p. 93), indicate that in all more advanced spiders the right palpus is applied to the right female orifice, and the left palpus to the left orifice. In Peucetia viridans, the paracymbium of the male palpus has a function in copulation that is quite unusual among spiders.5 The distal half of the paracymbium is two-pronged, the longer ventral process curving downward and forward from the outer side of the straight dorsal prong (Fig. 1). During copulation, the dorsal prong, probably acting as a guide, is inserted through the opening into the external tube of the female epigynum along with the embolus (which contains the seminal duct). The ventral prong fits over the outside of the epigynum, and the hook at its tip is received by a depression on the outer anterior part of the epigynum. This locks the paracymbium in place and limits the distance it can be inserted. The paracymbium is often broken off just proximal to its branching when the male withdraws the embolus. The epigynum probably is always covered with a "resinous" material after copulation, its origin yet unknown. Not all mated females exhibit this covering, which is easily removed and probably is sometimes lost during egg-laying. However, the epigyna of most mated females have
Bio-Évaluation De La Qualité Des Eaux De Surface D’oued Beht (Maroc) Indice Biologique Global Des Réseaux De Contrôle Et De Surveillance (IBG-RCS)

The present study concerns the biological assessment of Beht’s river quality in Morocco during the period Mai-June of 2014 using the standard Global Biological Index of Control and Surveillance Networks (GBICSN). Thus twelve sampling stations were chosen for the determination of the impact of agricultural and urban waste of Beht’s area on the biological waters quality of this river. As results this biological approach showed downgrading notes of the biological index from the watershed’s uphill to its downstream reflecting this way the deterioration of water quality with increasing anthropogenic action and inputs.
Inheritance of resistance to barley yellow dwarf virus detected by northern blot analysis. [Triticum aestivum L]

Development of wheat (Triticum aestivum L.) cultivars tolerant to the barley yellow dwarf virus disease (BYD) has been limited by lack of precision in rating plants for response to infection. In this study northern dot blot analysis was used to determine barley yellow dwarf virus (BYDV) RNA concentrations of six wheat cultivars that differed in visual BYD symptom expression
Functional analysis of epialleles in diploid and tetraploid Arabidopsis thaliana

Polyploidie, die Multiplikation des diploiden Chromosomensatzes, tritt bei Pflanzen haufig auf. Die Entstehung polyploider Pflanzen ist oft mit Anderungen ihrer Genom- als auch ihrer Epigenomorganisation verbunden. Die transkriptionelle Geninaktivierung (transcriptional gene silencing, TGS) fuhrt zu kompletten und erblichen Verlust der Expression vorher aktiver Gene. Durch TGS konnen Epiallele entstehen, die in ihrer DNA Sequenz ubereinstimmen, aber unterschiedlich exprimiert werden. Das inaktive Epiallel kann durch epigenetische Wechselwirkungen die aktive Form in trans beeinflussen, was zu einer epigenetischen Angleichung der beiden Epiallele fuhrt. Dieser Erbgang folgt nicht den Mendelschen Regeln und ahnelt der Paramutation. Da epigenetische Diversitat direkten Einfluss auf die phanotypische Vielfalt und den Wachstumserfolg von Pflanzen hat, sind die zugrundeliegenden, regulatorischen Mechanismen von groser Bedeutung fur naturliche Evolution und Pflanzenzuchtung. Die vorliegende Arbeit beschaftigt sich mit Prinzipien der polyploidie-assoziierten transkriptionellen Geninaktivierung (polyploidy-associated transcriptional gene silencing, paTGS) eines transgenen Resistenzgens (Hygromycinphosphotransferase, HPT), das in aktiven oder inaktiven Epiallel-Varianten in Arabidopsis thaliana auftritt. Um den paTGS-Mechanismus und die allelische Interaktion zu analysieren, habe ich die genetischen und epigenetischen Merkmale der Epiallele in diploidem und tetraploidem Hintergrund und nach Mutagenese charakterisiert. Die genetische Struktur der Epiallele wurde in Linien mit aktiven, inaktiven und strukturell veranderten HPT Genen untersucht. Ich konnte spezifische epigenetische Modifikationen (DNA-Methylierung und Histonmodifikationen) der Epiallele nachweisen. Da Paramutation in Mais im funktionellen Zusammenhang mit regulatorischen RNAs (small RNAs) steht, analysierte ich die Fahigkeit des Transgens, solche RNAs oder Antisense-Transkripte zu generieren. Zusatzlich wurde der Einfluss vieler epigenetischer Mutanten auf das inaktive Epiallel untersucht. In dieser Arbeit habe ich gezeigt, dass sich die beiden Epiallelformen in ihrer epigenetischen Zusammensetzung entsprechend ihrer Expressionsmuster, unterscheiden. Small RNAs oder Antisense-Transkripte durften bei der Regulation der Epiallele keine Rolle spielen. Verschiedene strukturelle Anderungen im inaktiven Epiallel fuhrten zur Reaktivierung der HPT Expression, was auf einen starken Einfluss der DNA Sequenz, vermutlich uber die Chromatinorganisation hindeutet.
Lycopene and Tomatoes in Human Nutrition and Health

Lycopene is a potent antioxidant carotenoid found in fruits and vegetables; particularly high amounts exist in red tomatoes. It is not an essential nutrient for humans but can be a potential agent for preventing some types of cancers. Recently there has been renewed interest in lycopene’s uses as an effective nutraceutical, playing roles in human nutrition and health. This book presents a comprehensive understanding of lycopene, focusing on its role in human nutrition, oxidative stress and chronic diseases.
Analysis of Rural Households Behavior in Case of Healthcare Expenditure Considering Income Deciles (Iran: 2009-2014)

This study is performed to compare healthcare expenditure patterns of different income deciles of Iranian rural households during 2009 to 2014. The econometric method is ordinary least square (OLS). Data is devised from National household survey data. It consists of healthcare expenditure, family income, the literacy level of parents, number of children and the average age of parents. This paper tries to quantify the degree of effectiveness of each variable on healthcare expenditure among different income deciles. It is also needed to examine if there is a statistically significant difference between effects of variables on healthcare expenditure during different income deciles. The findings verify that there is a significant difference in healthcare expenditure patterns between different income deciles. They show that in the first six deciles a similar pattern is observed. In these deciles, the level of education of parents doesn’t demonstrate a significant effect on the healthcare expenditure and a percent increase in the family income increases the healthcare expenditure less than 1%. Moreover, except for education level, other variables have a positive effect on the healthcare expenditure. Almost the same scheme is present on the remaining income deciles. Here, while literacy level of mother has a negative effect on healthcare expenditure, other variables including family income, average age of parents and number of children reveals a positive effect. These results could be interpreted as preventive effect of literacy level. Thus, in rural families, the contribution of mother to the management of healthcare expenditure is more effectual than father. On the other hand, ninth and tenth deciles indicate that a percent increase in family income, result in more than 1% increase in healthcare expenditure. Therefore, healthcare authorities are highly suggested to thrive to lift the awareness level of family. The same instruction could be to categorize base on the average age of parents. This could be performed via government agencies or insurance authorities.
Effect of rice bran mulching on growth and yield of cherry tomato. Cien. Inv. Agr. (In English) 34(3): 181-186.

From the spring to fall of 2005, in northern Kanto, located in central Japan, an open field was prepared for cultivating cherry tomatoes ( Lycopersicon esculentum var. cerasiforme ) with three types of mulch: 1. Rice straw with rice bran, 2. Rice straw alone, and 3. Polyethylene film covering. The fruits were harvested from June to the end of September. There were signifi cant differences between the treatments in both the total yield of fruit (p = 0.0379) as well as in the yield of normal fruit (p = 0.0458). The highest total fruit production (3.4 kg·plant -1 ) was obtained with the rice straw and bran treatment, followed by the other two treatments, with about 2.5 kg·plant -1 . Other factors, such as total fruit number and the weight of damaged fruit, were not significantly different. Forty days after planting in the field, plant height and other vegetative characteristics were measured; no statistically significant differences between the studied soil treatments were observed. These results indicate that the application of rice bran on a field surface previously covered with rice straw contributed to an increase in the yields of the tomato plants. The application of rice bran also facilitated weed control management. En la primavera al otono del ano 2005, en el norte de Kanto, localizado en el centro de Japon se preparo un area de campo para cultivar tomate de ramillete (tomate cherry ) (y Lycopersicon esculentum var. cerasiforme ) con tres tipos de cobertura: 1. Paja de arroz con salvado de arroz, 2. Paja de arroz solamente y 3. Cobertura con polietileno. La cosecha de los frutos se realizo desde junio hasta finales de septiembre. Hubo diferencias significativas entre los tratamientos, en el rendimiento total de los frutos (p = 0,0379) y el de frutos normales (p = 0,0458). Las mayores producciones de frutos totales (3,4 kg·planta -1 ) se obtuvieron con el tratamiento de paja de arroz con salvado de arroz, seguido por los otros dos tratamientos con alrededor de 2,5 kg·planta -1 . Los otros factores como el total de frutos y el peso de frutos danados no fueron significativamente diferentes. Despues de 40 dias de sembrado en el campo, se midio la altura de la planta y otros caracteres vegetativos sin obtener diferencias estadisticamente significativas entre los tratamientos del suelo estudiados. Los resultados indican que la aplicacion de salvado de arroz en la superficie del campo previamente cubierto con paja de arroz, para las plantas de tomate, contribuyen al incremento de los rendimientos. La aplicacion de salvado de arroz, tambien redujo el manejo para el control de malezas.
Web-based Versus Face-to-Face Interactionist Dynamic Assessment in Essay Writing Classrooms – A Comparative Study

The present mixed-method study attempted to investigate the efficacy of using an interactionist dynamic assessment procedure to assist university EFL learners in writing argumentative essays. It also sought to discover the differential effect of dynamic assessment in face-to-face versus web-based modes of delivering mediation. The quantitative component of the study revealed the outperformance of the experimental group on the posttest. However, the two modes of delivering mediation had no differential impact on the degree of improvement of the two experimental groups in the essay writing ability. Furthermore, with regard to the transfer tasks, the experimental groups could successfully transfer their learning to the near and far transfer tasks. The qualitative analysis of the negotiations also demonstrated an improvement in the essay writing ability of the participants over the sessions. Merging the quantitative and qualitative analyses, the study found that interactionist dynamic assessment, in both modes, can have positive effects on the learners’ ability to write better argumentative essays.
Perception and Action

The behaviorists considered perception (the stimulus) and action (the response) to be directly and sequentially linked, with one always leading to the other once the association has been learned. With the cognitive revolution, the separation between perception and action increased with the insertion of mental processes that take percepts as their inputs and use actions as their outputs. The cognitive revolution takes the computer as its analogy. A computer functions by processing inputs (perception), performing computations (cognition), and producing outputs (action). This dominant computer analogy–driven approach to cognitive psychology pushes the agenda that perception and action are at opposite ends (and perhaps the less important or exciting ends) of the serial processing of the mind. This cognitivism approach will be referred to as the see-think-act serial theory of the mind. That perception and action are at the ends of the cognitive spectrum should not lead to the assumption that these processes are simple or easy. Transforming external (e.g., optical) stimulation into conscious percepts
Edible Films of Blended Cassava Starch and Rice Flour with Sorbital and Their Mechanical Properties

In this study, the mechanical properties (tensile strength, elongation at break and folding resistance) of edible biopolymer film blends formed from blended cassava starch and rice flour at different compositions with sorbital used as a plasticizer. A suitable ratio of cassava starch and rice flour to water at 10% w/v was used to form a film solution. The addition of a plasticizer agent up to 30% w/w of blending compositions improved the mechanical properties of the generated films. The mechanical properties of the edible blended films with 30% plasticizer were strongly dependent on the blending compositions. Our results pointed out that the cassava starch and rice flour films at a ratio of 70:30 with sorbitol 30% (w/w) had the highest tensile strength which related to folding endurance of the films.
Breaking the Cycle? How (Not) to Use Political Finance Regulations to Counter Public Procurement Corruption

There are widespread perceptions and countless documented cases of tight-knit networks of politicians and businessmen colluding for allocating public procurement contracts in return for political party donations. In the absence of systematic evidence, neither the magnitude of the problem nor the effectiveness of policies curbing such corruption is well-understood. In order to advance our understanding of these phenomena, this paper tests whether political financing regulations can contribute to controlling corruption in public procurement. We utilize aggregated official micro-level data on almost 3 million contracts awarded across 29 European countries in 2009-2014 to measure the risk of high-level institutionalised corruption using novel proxy indicators. Legislation regulating political finances are directly measured by coding national laws in 2009-2014. In cross-country panel regression and difference-in-difference models, we find that introducing additional political financing restrictions does not have a measurable negative impact on public procurement corruption risks. In fact, the observed effect is positive in most models. The observed relationship remains the same for most constitutive components of political financing regulations. Several challenges remain for a conclusive judgement of political party financing regulations’ effectiveness to curb corruption such as measuring implementation rather than legislation, allowing for longer lead-time for regulatory impact, or considering institutional inter-dependencies.