Miracle-dz/UniFAR-FTUs huggingface dataset:
The Meaning of a Redundant Codon: There is Protein Folding Information in Nucleic Acids in Addition to the Genetic Code

All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, which is not represented by the known genetic code. Nucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE) than the subsequence containing only the 2nd residues (p<0.0001, n=81). This periodic FFE difference is not present in introns and therefore it is a specific physico-chemical characteristic of coding sequences and it might contribute to unambiguous definition of codon boundaries during translation. The FFE in the 1st and 3rd residues is additive, which suggests that these residues contain a significant number of complementary bases and contribute to selection for local RNA secondary structures in coding regions. This periodic, codon-related structure-forming of mRNAs indicates a connection between the structure of exons and the corresponding (translated) proteins. The folding energy dot plots of RNAs and the residue contact maps of the coded proteins are indeed similar. Residue contact statistics using 81 different protein structures confirmed that amino acids that are coded by partially reverse and complementary codons (Watson-Crick (WC) base pairs at the 1st and 3rd codon positions and translated in reverse orientation) are preferentially co-located in protein structures. Exons are distinguished from introns and codon boundaries are physico-chemically defined by periodically distributed FFE differences between codon positions. There is a selection for local RNA secondary structures in coding regions and this nucleic acid structure resembles the folding profiles of the coded proteins. The preferentially (specifically) interacting amino acids are coded by partially complementary codons, which strongly supports the connection between mRNA and the corresponding protein structures and indicates that there is protein folding information in nucleic acids that is not present in the genetic code. This might give some additional explanation of codon redundancy.
Long-term trends in the distribution of phytoplankton in Chesapeake Bay: roles of light, nutrients and streamflow

This paper synthesizes >40 yr of data on phytoplankton abundance in the Chesapeake Bay, USA, spanning the period 1950 to 1990. Long-term changes in the concentrations of surface chlorophyll (B, mg m-3) and integrated water-column chlorophyll (B',,, mg m-2) are assessed in the context of light and nutrient effects on phytoplankton distributions. Significant long-term increases in B were detected from the 1950s to the 1970s in all regions of the Bay. The seaward, polyhaline Bay showed increases in B of 300 to 500%, while mesohaline and oligohaline values increased by between 40 and nearly 400%. Annual means for recent years, 1985-90, showed interannual variations of ca 80%, but trends of the magnitude observed for 1950-70 were not detected. Frequency distributions of B showed shifts in overall distributions to higher values, particularly in the lower, polyhaline Bay where the frequency of B < 2 mg m-3 in the 1950s and 1960s was much higher than in 1985-90. B',,, data showed the apparent lack of a winter-spring maximum of contemporary proportions in the 1960s, in contrast to data from the 1970s, early 1980s and 1985-90 that show a well-developed peak in B',,, for most of these years. Nutrient concentrations and ratios have also changed significantly since the 1960s. Concentrations of dissolved inorganic nitrogen (DIN) in the oligohaline Bay have approximately doubled in the past 20 to 30 yr, wMe orthophosphate (Pod3-) concentrations have generally declined, producing a change in DIN: POA3with rarmfications for nutrient limitation in the Bay. These results are discussed in the context of the regulation of interannual variations m the timing, position and magnitude of the winter-spring phytoplankton bloom in the Bay by freshwater flow from the Susquehanna River.
A move-step analysis of the concluding chapters in computer science phd theses

espanolEste articulo describe como los autores de tesis doctorales en el area de la informatica elaboran los capitulos de conclusion. Los datos proceden de los capitulos finales de 48 tesis doctorales defendidas en la Universidad de Glasgow entre 2008 y 2014. Para el analisis se siguio un enfoque cualitativo y cuantitativo. En una primera etapa, se examinaron los titulos de los capitulos de conclusion de las tesis asi como sus divisiones en secciones y subsecciones. Posteriormente, se analizaron los capitulos atendiendo a unidades informativas organizadas en movimientos y pasos: Movimiento 1 (M1) “Revision del estudio”; Movimiento 2 (M2) “Consolidacion del espacio de investigacion”; Movimiento 3 (M3) “Propuesta de aplicaciones practicas e implicaciones”, Movimiento 4 (M4) “Recomendaciones para futuras investigaciones” y Movimiento 5 (M5) “Recapitulacion del estudio”. Los resultados indican que la mayoria de las tesis de este corpus de informatica tiene un unico capitulo final de conclusiones con tres movimientos principales: M1, M2 y M4. Los pasos mas frecuentes consisten en “revisar el trabajo llevado a cabo” y “resumir el trabajo especifico desarrollado en cada capitulo de la tesis” en M1, “enunciar los resultados y las contribuciones en respuesta a las hipotesis y preguntas iniciales” y “reivindicar su aportacion” en M2, y “reconocer limitaciones de la investigacion” y “sugerir investigaciones futuras” en M4. La practica habitual consiste en utilizar patrones de movimientos y pasos en ciclos recurrentes a lo largo de la conclusion. Se aportan sugerencias con fines pedagogicos EnglishThis paper describes how computer science doctoral writers construct the closing chapters of their PhD theses. The data are drawn from the chapters playing a concluding role of 48 PhD theses defended at the University of Glasgow from 2008 to 2014. The analysis applied a qualitative-quantitative approach. The titles of the concluding chapters of the theses were first examined and also their divisions into sections and sub-sections. Then the chapters were subjected to a move-step analysis: Move 1 (M1) “Revisiting the study”; Move 2 (M2) “Consolidating research space”; Move 3 (M3) “Proposing practical applications and implications”, Move 4 (M4) “Recommending future work” and Move 5 (M5) “Recapitulating the study”. The results revealed that most of the computer science PhD theses have one final concluding chapter with three main moves: M1, M2 and M4. The most frequent steps are “reviewing the work carried out” and “summarizing the specific work reported in every thesis chapter” in M1, “presenting results and contributions”, “answering the initial research questions or hypotheses”, and “making claims” in M2, and “acknowledging limitations” and “suggesting further research” in M4. Movestep patterns appear in recurrent cycles throughout the concluding chapters. Several suggestions for pedagogical purposes are provided
Solid state fermentation studies of citric acid production

Treated sugarcane bagasse supplemented with sucrose medium was found 1.7 fold (citric acid based on sugar consumption) better substrate than untreated bagasse carrier. The performance of packed bed reactor at aeration rate of 0.75 l/min and apparent packing density of 35.0 g/l was superior with citric acid yield of 55.90% (w/w), overall productivity of 0.087 g/100 g DS.h and specific growth rate of 0.055 h-1. However, in flask fermentation citric acid yield of 41.56% (w/w) with overall productivity of 0.064 g/100 gDS.h and specific growth rate of 0.043 h-1 was observed. The system confirmed that citric acid production was Type-II fermentation. Citric acid recovery of 90.39% (w/w) was achieved from fermented broth.
Primary root growth, tissue expression and co-expression analysis of a receptor kinase mutant in Arabidopsis

There is no functional annotation for the majority of the several hundreds of receptor-like kinases in plants. A direct way of inferring the function of these proteins is to study the phenotype that results from loss of function mutants such as T-DNA mutant lines. In this research a function (phenotype) to At2g37050 gene that encodes a receptor like kinase in Arabidopsis T-DNA line was assigned. This phenotype has a shorter primary root length at later stages of development. Transcription study of the gene showed some tissue specificity with more expression level in the root in comparison with other tissues. To study genes co-expressed with At2g37050, ATTED-II web tool was used. It was found that the CLASP gene is co-expressed with At2g37050 with a Pearson correlation > 0.6. In kinematic analysis of the difference in root growth, the length between the root tip and the first epidermal cell with a visible root hair bulge for 8 day-old seedlings of wild type plants was 1327± 76.50 µm (n=6) and for the mutant plants, was 1109± 72.28. This parameter of the wild type and the mutant plants shows that loose of function of At2g37050 gene, reduce cell elongation in the elongation zone of root.
Using Taxes to Manage a Multigear Fishery: An Application to a Spanish Fishery

When fishing gears alter the composition of fish populations or modify the recruitment rate, it is advisable to include the degree of their fishing selectivity in the analysis. Fishing selectivity can cause two different management problems: interspecies selectivity or by‐catch of fish stocks for which no quota has been set by the regulator. The case study is the Spanish fishery of hake ( Merlucius merlucius ), where the fleet operates using two main gears; most of the vessels are trawlers but a few boats use longlines and other fixed gears. Fishery management by means of effort taxes and how the degree of intraspecies selectivity may affect the resource and tax levels are analyzed. The results show that the tax level will depend on the social value of the marine stock, the marginal productivity of each fleet's effort, and the effect that the fishing activity of each one has on the growth of the hake biomass.
Disconnected Julia set and rotation sets

- Let ^ be the conformal isomorphism from the complement of the unit disc to the complement of the Mandelbrot set M. We study the map ^ at the roots of the hyperbolic components of M. It is shown that the function (log \w — wol""" 1 )"" 1 describes ^ at each periodic point WQ of the map w ! —>• w 2 .
Comparable Domain Dependency in Sentiment Analysis

Sentiment analysis (or opinion mining) is concerned not with the topic of a document, or its factual content, but rather with the opinion expressed in a document. In this paper we present a number of experiments on a word-based sentiment analysis on two corpora representing two related domains: film reviews and book reviews. We find that even close domains are very difficult to process without utilising in-domain data. We also indicate certain characteristics of features that affect cross-domain performance of sentiment classifiers.
Meat demand flexibilities for Tanzania: Implications for the choice of long-term investment

This study uses the inverse almost ideal demand system (IAIDS) to estimate demand flexibilities for beef, small ruminant (sheep and goat) meat, pork and poultry in Tanzania. Own uncompensated price flexibilities were less than one in absolute value, implying that both direct and indirect induced price effect through a change in total expenditure have little impact on budget shares. Estimated scale flexibilities were all negative, suggesting that increases in income will increase the quantities of meat consumed. Production of small ruminant meat was the most attractive investment compared to other meat commodities.
Monoclonal antibody against Rab8 from Bombyx mori (Lepidoptera: Bombycidae)

Small GTPases of the Rab family are key regulators of membrane trafficking. Monoclonal antibodies are useful tools for identifying proteins that interact with other proteins and for examining their tissue distribution. We selected a monoclonal antibody against Rab8 of Bombyx mori L. It specifically recognized amino acid residues 30-109, which are conserved among Rab8 proteins, and did not recognize any other Rab proteins. Western blotting using the antibody revealed one band in the brains of B. mori and rat. Far-Western blotting analysis detected three proteins interacting with Rab8. These results indicate that this antibody is useful for clarifying the physiological function of Rab8 of B. mori and other species. This is a report of a study on a monoclonal antibody against insect Rab protein.
IZA Discussion Paper No. 433

Protective or Counter-Productive? Labor Market Institutions and the Effect of Immigration on EU Natives We estimate the effect of immigrant flows on native employment in Western Europe, and then ask whether the employment consequences of immigration vary with institutions that affect labor market flexibility. Reduced flexibility may protect natives from immigrant competition in the near term, but our theoretical framework suggests that reduced flexibility is likely to increase the negative impact of immigration on equilibrium employment. In models without interactions, OLS estimates for a panel of European countries in the 1980s and 1990s show small, mostly negative immigration effects. To reduce bias from the possible endogeneity of immigration flows, we use the fact that many immigrants arriving after 1991 were refugees from the Balkan wars. An IV strategy based on variation in the number of immigrants from former Yugoslavia generates larger though mostly insignificant negative estimates. We then estimate models allowing interactions between the employment response to immigration and institutional characteristics including business entry costs. These results, limited to the sample of native men, generally suggest that reduced flexibility increases the negative impact of immigration. Many of the estimated interaction terms are significant, and imply a significant negative effect on employment in countries with restrictive institutions. JEL Classification: J23, J61, O52
Itraconazole loaded ethosomal gel system for efficient treatment of skin cancer

Topical application of Itraconazole for the treatment of Basal cell carcinoma represents a new hope in dermatology. Itraconazole for treatment of Basal cell carcinoma is an alternative therapeutic approach for the efﬁcacious treatment of nonmelanoma skin cancer. Itraconazole loaded ethosomes were prepared and characterized by vesicular shape, vesicular size, entrapment eﬃciency. Ethosomal gel were prepared and characterized by pH, viscosity, washability, spreadibility, drug content, drug release study, stability study, in vivo skin tolerability and antiproliferative activity. Transmission Electron Microscopy (TEM), and Dynamic Light Scattering (DLS) characterise ethosomes as spherical, unilamellar structures having low polydispersity (0.384 ± 0.037) and nanometric size range (169.0 ± 49.0), % Entrapment eﬃciency of Itraconazole in ethosomal carrier was found to be 82.00 ± 1.78. Ethosomal gel were prepared by using Carbopol. The viscosity was found to be in the range of 1600±1.72 to 1740±1.73 cps. The spreadability was found to be in the range of 6.4g. cm/sec. The drug content of the ethosomal gel formulations ranged from 0.384-0.386 mg/gm. The value of steady-state transdermal ﬂux was observed to be 54.2 ± 1.46 µg/h/cm with a lag time of 1.2 hrs with formulation EG1. Stability studies revealed no noticeable changes in drug release profile occurred. Skin irritation study on rabbit skin suggested that ethosomal gel may oﬀer a suitable approach for transdermal delivery of Itraconazole. The further, antiproliferative study shows that Itraconazole loaded ethosomes is significantly more toxic than the free drug on BCC1/KMC cell line, thus making it a potential alternative to the standard therapy.
Monetary Policy Rules for a Developing Countries: Evidence from Tunisia

This paper estimates the forward-looking monetary policy reaction function of the Central Bank of Tunisia (CBT) using quarterly data from 1993:Q2 to 2011:Q4. Policies which the CBT applied are analyzed according to the Taylor rule. The empirical results indicate that the CBT followed the Taylor rule in its interest setting behaviour. In forward-looking models, the response coefficient of expected inflation is greater than of the output gap, which is consistent with the fact that inflation is the primary objective of monetary policy. The results of forward-looking models reflect the policies conducted in Tunisia .
Multi-objective ship's cargo handling model

This paper proposes a new optimization model for ship's cargo handling operations which solution gives the structure of cargo handling resources required, along with attaining the minimum total ‘in-port’ costs and the minimum of time required for completion of cargo operations. Due to complexity of the model which consists of composite multi-objective functions together with several decision variables and constraints, the solution has been sought by utilization of an adapted genetic algorithm combined with a hybrid algorithm. Testing of the model on real world data yielded acceptable results in a short time. In the course of decision making, the ship's operator can, on the basis of the proposed model and taking into consideration shipping market data, choose appropriate variation of the returned solution, which incorporates minimum costs, minimum of operational time and related cargo handling resources.
Contesting Power: Food Sovereignty as Pedagogical Practice and Resistance

in the colonial food regime (McMichael, 2009). This regime, and those that have followed it, is based on Western science or ‘monocultures of knowledge’ granted ‘epistemological privilege’ from the seventeenth century (Santos, 2008). Modern science effectively suppressed subaltern knowledges and practices, laying a foundation for the domination of the global North in food production systems. Countering this dominance, La Vía Campesina has emerged as the most prominent rural-based movement to recognize and promote the immense diversity of e pistemologies among its constituents. Members of the movement center this at the heart of their resistance against the corporate food regime through the concept of food sovereignty, or soberania alimentaria. For peasant farmer organisations in countries such as Brazil, the focus of this article, food sovereignty is a radical proposal for social transformation that aspires to democratise food systems using the concept of ‘agroecology’ to construct ‘an alternative value system’ (Meek, 2014, p. 48). Agroecology, defined as ‘a way of redesigning food systems, from the farm to the table, with a goal of achieving ecology, economic, and social sustainability’ (Gliessman, 2016, p. 187), is widely cited by a growing number of international agricultural experts to be a viable solution to a conventional production model that is resource-intensive and environmentally destructive (Valenzuela, 2016). More than a technical program, it is part of a larger movement toward an ‘emancipatory rural politics’ (Scoones et al., 2017). This paper explores how agro ecological knowledge is transmitted through ‘transdisciplinary, participatory, and change-oriented research and action’ (Gliessman, 2015) in a National School of Agroecology (Instituto Agroecologico Latinamericanos, IALA) in Brazil under the remit of the Landless Workers Movement (Moimento dos Trabalhadores Rurais Sem terra, MST). In this School resistive pedagogical and communication models are applied with the aim of developing students as technically proficient, politicised individuals who can help their communities make the shift to ecological farming. Embodying a post-colonial politics, ‘new ethics’ and praxis based on moral economy and agroecological values, these methods provide a direct contrast to the vertical dissemination or top-down modes of operation witnessed in conventional agronomy education that supports the corporate food system.
AMOVA ["Accumulative Manifold Validation Analysis"]: An Advanced Statistical Methodology Designed to Measure and Test the Validity, Reliability, and Overall Efficacy of Inquiry-Based Psychometric Instruments.

This monograph provides an epistemological rational for the Accumulative Manifold Validation Analysis [also referred by the acronym “AMOVA”] statistical methodology designed to test psychometric instruments. This form of inquiry is a form of mathematical optimization in the discipline of linear stochastic modelling. AMOVA is an in–depth statistical procedure for the internal testing of research instruments based on the metrics from the novel “Taxonomy of Process Education”. The Taxonomy of Process Education (TPE) is based off of the Process Education (PE), four–level measures designed to measure self–growth. The PE four levels in particular are viewed as sequential stages (or phases) of professional development. The four levels are also constructed to build towards the highest level of content knowledge or subject matter expertise (Pacific Crest, 2015). The TPE metric has universal applicability and is ideally suited for weighted mathematical measurement of content (subject matter), knowledge (cognitive), disposition (affective), and capability (psychomotor). This original methodology is a novel approach to advanced statistical post hoc data analysis. It adds considerable value to the methods designed to assess instrument validity and reliability especially when said instrumentation is researcher–designed. A sequential AMOVA mathematical model is provided (for sample data “Crosswise–Validation Analysis”) along with its associated PE Taxonomy and measurement metrics in a step-by-step fashion that illustrates the entire process of advanced instrument validation inquiry.
Ecosystem-Based Agriculture Combining Production and Conservation—A Viable Way to Feed the World in the Long Term?

This study analyzed examples of sustainable ecosystem-based agriculture where management methods supported livelihoods of smallholders while at the same time local ecosystem services were enhanced in Ethiopia, Brazil, and the Philippines. Participation by farmers and collective actions were found to be a crucial driving force, as local specific knowledge and “learning by doing” were main components of the development. Social cohesion, particularly through associations and cooperatives, and improved marketing opportunities were also important drivers. Furthermore, recognition by authorities at all levels was perceived as crucial. Effects of climate change, insecure property rights, and political instability were potential threats. The possibilities of such systems to be scaled up beyond self-sufficiency raised further questions.
Coherent mode of a high intensity beam in a synchrotron

As one of major sources which cause emittance growth and beam loss in high intensity hadron synchrotrons, we have investigated coherent mode oscillations in a beam. Using Sacherer's (1968) envelope equations, mode frequencies of a bunched beam are derived. Multi-particle simulation shows that emittance growth occurs when the oscillation frequency of a coherent mode hits a resonance. The present status of a beam experiment at HIMAC is also mentioned, which is expected to show the direct observation of a resonance crossing of a coherent mode and beam loss.