Miracle-dz/UniFAR-FTUs huggingface dataset:
The structural basis of molecular adaptation.

The study of molecular adaptation has long been fraught with difficulties, not the least of which is identifying out of hundreds of amino acid replacements those few directly responsible for major adaptations. Six studies are used to illustrate how phylogenies, site-directed mutagenesis, and a knowledge of protein structure combine to provide much deeper insights into the adaptive process than has hitherto been possible. Ancient genes can be reconstructed, and the phenotypes can be compared to modern proteins. Out of hundreds of amino acid replacements accumulated over billions of years those few responsible for discriminating between alternative substrates are identified. An amino acid replacement of modest effect at the molecular level causes a dramatic expansion in an ecological niche. These and other topics are creating the emerging field of "paleomolecular biochemistry. "
Phylogenetic relationships of freshwater fishes of the genus Capoeta (Actinopterygii, Cyprinidae) in Iran

Abstract The Middle East contains a great diversity of Capoeta species, but their taxonomy remains poorly described. We used mitochondrial history to examine diversity of the algae‐scraping cyprinid Capoeta in Iran, applying the species‐delimiting approaches General Mixed Yule‐Coalescent (GMYC) and Poisson Tree Process (PTP) as well as haplotype network analyses. Using the BEAST program, we also examined temporal divergence patterns of Capoeta. The monophyly of the genus and the existence of three previously described main clades (Mesopotamian, Anatolian‐Iranian, and Aralo‐Caspian) were confirmed. However, the phylogeny proposed novel taxonomic findings within Capoeta. Results of GMYC, bPTP, and phylogenetic analyses were similar and suggested that species diversity in Iran is currently underestimated. At least four candidate species, Capoeta sp4, Capoeta sp5, Capoeta sp6, and Capoeta sp7, are awaiting description. Capoeta capoeta comprises a species complex with distinct genetic lineages. The divergence times of the three main Capoeta clades are estimated to have occurred around 15.6–12.4 Mya, consistent with a Mio‐Pleistocene origin of the diversity of Capoeta in Iran. The changes in Caspian Sea levels associated with climate fluctuations and geomorphological events such as the uplift of the Zagros and Alborz Mountains may account for the complex speciation patterns in Capoeta in Iran.
Supporting international students through strengthening their social resources

Efforts to recruit international students to higher education must be matched with preparation of the campus community for engaging with this diverse population. The motives of international students for pursuing international studies, including academic and career goals, are facilitated through building strong relationships with members of the host institution. The social integration of international students is important for their academic performance, for building a sense of connection to the destination country, and for supporting career plans post-graduation. Three key social resources for supporting international student transitions include academic faculty, counsellors, and local students. However, these groups need to be prepared to support international students through a high-quality educational experience and through addressing the demands of living and learning in a new cultural and academic environment. Engagement with international students is critical for their success and offers unique relationships to increase the cross-cultural learning of all members of the campus community.
Identification and Characterization of an S-Adenosyl-L-methionine:-Sterol-C-methyltransferase cDNA from Soybean (*)

In plants, the dominant sterols are 24-alkyl sterols, which play multiple roles in plant growth and development, i.e. as membrane constituents and as precursors to steroid growth regulators such as brassinosteroids. The initial step in the conversion of the phytosterol intermediate cycloartenol to the 24-alkyl sterols is catalyzed by S-adenosyl-L-methionine:Δ-sterol-C-methyltransferase (SMT), a rate-limiting enzyme for phytosterol biosynthesis. A cDNA clone (SMT1) encoding soybean SMT was isolated from an etiolated hypocotyl cDNA library by immunoscreening using an anti-(plasma membrane) serum. The deduced amino acid sequence of the SMT1 cDNA contained three conserved regions found in S-adenosyl-L-methionine-dependent methyltransferases. The overall structure of the polypeptide encoded by the SMT1 cDNA is most similar to the predicted amino acid sequence of the yeast ERG6 gene, the putative SMT structural gene. The polypeptide encoded by the SMT1 cDNA was expressed as a fusion protein in Escherichia coli and shown to possess SMT activity. The growing soybean vegetative tissues had higher levels of SMT transcript than mature vegetative tissues. Young pods and immature seeds had very low levels of the SMT transcript. The SMT transcript was highly expressed in flowers. The expression of SMT transcript was suppressed in soybean cell suspension cultures treated with yeast elicitor. The transcriptional regulation of SMT in phytosterol biosynthesis is discussed.
Cellular and genetic control of antibody responses. V. Helper T-cell recognition of H-2 determinants on accessory cells but not B cells

Requirements for helper T-cell recognition of H-2 determinants expressed on adherent accessory cells and on B cells was individually assessed in the anti-hapten PFC responses to TNP-KLH. Complicating allogeneic effects were minimized or avoided by the use of helper T cells from normal F1 hybrids, parent leads to F1 chimeras, and F1 leads to parent chimeras. The results of both in vitro and in vivo experiments demonstrated that: (a) helper T cells are not required to recognize the identical H-2 determinants on both accessory cells and B cells; (b) helper T cells are required to recognize K or I-A region- encoded determinants expressed on accessory cells; (c) no requirement was observed in vitro or in vivo for helper T-cell recognition of B- cell-expressed H-2 determinants; and (d) no requirement was observed for H-2 homology between accessory cells and B cells. The absence of required helper T-cell recognition of the identical H-2 determinants on both accessory cells and B cells was demonstrated in two ways: (a) naive of KLH-primed (A x B)F1 hybrid helper T cells collaborated equally well with B cells from either parentA or parentB in the presence of accessory cells from either parent; (b) A leads to (A x B)F1 chimeric spleen cells depleted of accessory cells collaborated equally well with accessory cells from either parentA or parentB, even though the B cells only expressed the H-2 determinants of parentA. A requirement for helper T-cell recognition of K or I-A region-encoded H- 2 determinants on accessory cells was also demonstrated in two ways: (a) (A x B)F1 leads to parentA chimeric spleen cells depleted of accessory cells collaborated with accessory cells from parentA but not parentB; and (b) (A x B)F1 leads to parentA chimeric helper T cells collaborated with normal F1 B cells only in the presence of parental or recombinant accessory cells that expressed the K or I-A region-encoded determinants of parentA. Although restricted in their ability to recognize H-2 determinants on accessory cells, it was demonstrated both in vitro and in vivo that (A x B)F1 leads to parentA chimeric helper T cells were able to collaborate with B cells from either parentA or parentB. In vitro in the presence of accessory cells from parentA, (A x B)F1 leads to parentA chimeric helper T cells collaborated equally well with B cells from either parent. In addition, the inability of (A x B)F1 leads to parentA chimeric helper T cells to collaborate with (B + accessory) cells from parentB was successfully reversed by the addition of parentA SAC as added accessory cells. In vivo, upon the addition of parentA accessory cells, (A x B)F1 leads to parentA chimeric helper T cells collaborated with parentB B cells in short-term adoptive transfer experiments.
Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function

The proposed Drosophila melanogaster L23a ribosomal protein features a conserved C-terminal amino acid signature characteristic of other L23a family members and a unique N-terminal extension [Koyama et al. (Poly(ADP-ribose) polymerase interacts with novel Drosophila ribosomal proteins, L22 and l23a, with unique histone-like amino-terminal extensions. Gene 1999; 226: 339–345)], absent from Saccharomyces cerevisiae L25 that nearly doubles the size of fly L23a. The ability of fly L23a to replace the role of yeast L25 in ribosome biogenesis was determined by creating a yeast strain carrying an L25 chromosomal gene disruption and a plasmid-encoded FLAG-tagged L23a gene. Though affected by a reduced growth rate, the strain is dependent on fly L23a-FLAG function for survival and growth, demonstrating functional compatibility between the fly and yeast proteins. Pulse-chase experiments reveal a delay in rRNA processing kinetics, most notably at a late cleavage step that converts precursor 27S rRNA into mature 25S rRNA, likely contributing to the strain's slower growth pattern. Yet, given the essential requirement for L23(a)/L25 in ribosome biogenesis, there is a remarkable tolerance for accommodating the fly L23a N-terminal extension within the structure of the yeast ribosome. A search of available databases shows that the unique N-terminal extension is shared by multiple insect lineages. An evolutionary perspective on L23a structure and function within insect lineages is discussed.
Computing with hybrid CMOS/STO circuits

Recent research in spin torque nano-oscillators (STNO) have opened the possibility of using electron spin to generate sustained microwave oscillations. Furthermore, the experimental verification of synchronization of STNOs could allow communication and computation with nanoscaled oscillators. In this paper, we propose a hybrid MOSFET/STNO array which can be used for pattern recognition applications. First, we show that an array of electrically coupled STNOs obey the dynamics of Kuramoto's weakly coupled oscillators [1]. This behavior allows us to use the STNO array to implement the oscillatory neurocomputer proposed by Hoppensteadt et. al. [2]. We next consider practical STNO device geometries which can be used in a parallel-connected array. We propose using a dual barrier magnetic tunnel junction (DMTJ) to produce strong, harmonic oscillation signals in the absence on an external magnetic field. Finally, we perform HSPICE simulations of a hybrid MOSFET/STNO array to show how it can be used for pattern recognition.
Alos PALSAR polarimetric data for land use / land cover classification in Amazon

This research is an investigation on how the use of multi polarized data (HH,VV,HV) improves, or not, the land cover classification when compared with the standard two/one channels products. The well known Tapajos National Forest, in the Brazilian Amazon, Pará State, was the study area. Several supervised classifiers have been used, to have, as much as possible, a classifier independent assessment.
Swarm Intelligence for Feature Identification in Natural Terrain Environment

One of the most important problems in remote sensing studies is the classification of features in the satellite images, as it provides land use/ land cover information of the area under study. The Land Cover information like vegetation, water bodies, rocky area, sandy area etc. and its change over a period of time greatly affect local, regional and global environmental changes. Land Use information like buildings, roads and railway tracks are important features of urban infrastructure which crucially affect the life of people in cities. Recent developments in biologically inspired optimization techniques have motivated the researchers to explore the application of these techniques to the problem of satellite image feature classification. In this paper particle swarm optimization (PSO) along with the morphological operators is used for the identification of urban features like road and railway network, as well as land cover types, contained in the image. The concept of this paper is to explore and utilize the neighborhood information of the swarm computing algorithm to accurately identify features in the natural terrain environment. The test areas used are located in urban environment of Chandigarh and Saharanpur. Google Earth images of these areas were acquired and processed. The approach adopted has yielded satisfactory results.
Nonlinear System Modelling Via Optimal Design Of Neural Trees

This paper introduces a flexible neural tree model. The model is computed as a flexible multi-layer feed-forward neural network. A hybrid learning/evolutionary approach to automatically optimize the neural tree model is also proposed. The approach includes a modified probabilistic incremental program evolution algorithm (MPIPE) to evolve and determine a optimal structure of the neural tree and a parameter learning algorithm to optimize the free parameters embedded in the neural tree. The performance and effectiveness of the proposed method are evaluated using function approximation, time series prediction and system identification problems and compared with the related methods.
FO4-based models for area, delay and energy of polynomial multiplication over binary fields

Accurate mathematical models are crucial for design and evaluation of systems and architectures. To provide models that can accurately describe polynomial multipliers in F2[x], we integrate the traditional gate-counting method and the fanout four (FO4) model. We show that the resulting model provides much more accurate estimates than the traditional model and can be obtained by straight-forward modification to the traditional models. Implementation results indicate that the conventional gate delay model has 40% error, while the presented model has less than 4% error. We also show that the ceiling function, conventionally used in delay equations, are not needed in the new model. Moreover, we give a model for the energy consumption of polynomial multiplication, which can be used to estimate power consumption of finite field multiplication. To evaluate the accuracy of our models, we provide ASIC implementation results and compare them to results obtained from models.
Oenothein B, a Cyclic Dimeric Ellagitannin Isolated from Epilobium angustifolium, Enhances IFNγ Production by Lymphocytes

Oenothein B is a polyphenol isolated from Epilobium angustifolium and other plant sources, which has been reported to exhibit immunomodulatory properties. Oenothein B is known to activate myeloid cells and induce the production of IL-1 and other cytokines. However, its effects on lymphocytes are unknown. In this report, we show that oenothein B stimulated innate lymphocytes, including bovine and human γδ T cells and NK cells, resulting in either increased CD25 and/or CD69 expression. We also demonstrate that oenothein B enhanced the production of interferon-γ (IFNγ) by bovine and human NK cells alone and in combination with interleukin-18 (IL-18), a response not observed with other commonly studied polyphenols. Furthermore, we demonstrate that oenothein B enhanced the production of IFNγ by human T cells. Since IFNγ contributes to antitumor, antibacterial, and antiviral cell responses, these data suggest an additional mechanism that could account, at least in part, for the immune enhancing properties of oenothein B.
Blended learning with everyday technologies to activate students ' collaborative learning

Schools are facing challenges to meet the demands of the information society and the student generation of today. Not only are students carrying their mobile phones everywhere, they are also familiar with different online environments, especially social software. This situation can be seen both a challenge and a chance for schools, as mobile techn ologies and social software can be used as tools for building flexible learning environments to foster students ’collaborative learning. This paper examines the possibilities of mobile technologies and social software in the contexts of blended learning and collaborative learning theories. The paper also provides two concrete examples of how these possibilities have been put into practice in higher education, namely teacher education. It provides ideas for the use of mobile technologies and social software in teaching and learning .
The Capacity Region for Broadcast Channels with Conditionally Independent Message Sets

A more general class of broadcast channels with conditionally independent message sets is defined and its capacity region is determined using Marton 's inner bound and the outer bound considered by Nair and El Gamal. The capacity region for this class of channels includes the capacity region for broadcast channels with degraded message sets, semi-deterministic broadcast channels, deterministic broadcast channels with and without common information, less noisy and (special) more capable broadcast channels.
Approach of Information Retrieval with Reference Corpus to Novelty Detection

According to the results of TREC 2002, we realized the major challenge issue of recognizing relevant sentences is a lack of information used in similarity computation among sentences. In TREC 2003, NTU attempts to find relevant and novel information based on variants of employing information retrieval (IR) system. We call this methodology IR with reference corpus, which can also be considered an information expansion of sentences. A sentence is considered as a query of a reference corpus, and similarity between sentences is measured in terms of the weighting vectors of document lists ranked by IR systems. Basically, we looked for relevant sentences by comparing their results on a certain information retrieval system. Two sentences are regarded as similar if they are related to the similar document lists returned by IR system. In novelty parts, similar analysis is used to compare each relevant sentence with all those that preceded it to find out novelty. An effectively dynamic threshold setting which is based on what percentage of relevant sentences is within a relevant document is presented. In this paper, we paid attention to three points: first, how to use the results of IR system to compare the similarity between sentences; second, how to filter out the redundant sentences; third, how to determine appropriate relevance and novelty threshold.
Analysis of the scientific literature on Massive Open Online Courses (MOOCs)

Massive Open Online Courses (MOOCs) have been gaining attention from Academy by the disruptive innovation with which technology is brought into the educational system. Due to the emergence of the theme, the area needs recent bibliometric studies that point at previous studies about it and indicate directions for further research. Therefore, this study aims to map MOOC researches on published until December 2014 in two scientific databases: Scopus and Web of Science. Relevant aspects of scientific literature on MOOCs were explored from the collected data such as: (i) the number of publications per year; (ii) mapping of the institutions; (iii) authors with the most publications; (iv) classification in macro-theme of the identified jobs and (v) references most used by the authors. For the analysis, it was used 294 papers written by 694 authors, affiliated with 266 institutions. In the articles analysed, the authors used 5,060 different references, as well as 634 different keywords. This work, in addition to a mapping of research, aims to contribute to the spreading of the idea that the MOOC theme is emerging, promising and it needs to go further in the development of new researches.
Almost Isoperimetric Subsets of the Discrete Cube

We show that a set A ⊂ {0, 1}n with edge-boundary of size at most \[|A| (\log_{2}(2^{n}/|A|) + \epsilon)\] can be made into a subcube by at most (2ε/log2(1/ε))|A| additions and deletions, provided ε is less than an absolute constant. We deduce that if A ⊂ {0, 1}n has size 2t for some t ∈ ℕ, and cannot be made into a subcube by fewer than δ|A| additions and deletions, then its edge-boundary has size at least \[|A| \log_{2}(2^{n}/|A|) + |A| \delta \log_{2}(1/\delta) = 2^{t}(n-t+\delta \log_{2}(1/\delta)),\] provided δ is less than an absolute constant. This is sharp whenever δ = 1/2j for some j ∈ {1, 2, . , t}.
Mitigating occupational stress: The role of psychological capital

ABSTRACT This study examined the impact of occupational stress on psychological well-being looking at the mediating role of psychological capital (PsyCap) in the occupational stress and psychological well-being relationship. Using a cross-sectional survey design, data was collected from 290 participants. The collected data was analyzed using a Pearson r test and hierarchical regression. Analysis of the data showed that psychological well-being (PWB) related negatively with occupational stress and positively with PsyCap. It was also found that PsyCap mediated fully the relationship between occupational stress and PWB thereby rendering nonsignificant the negative effects of occupational stress on PWB. In addition, the study found that, efficacy, hope, resilience, and optimism (components of PsyCap) mediated partially the occupational stress–PWB relationship thereby reducing the negative effect of occupational stress on psychological well-being. It is concluded that PsyCap has the ability to buffer the negative consequences of occupational stress on psychological well-being.
Transcription work: learning through coparticipation in research practices

The focus for this paper evolved out of doctoral research conducted by the author with incarcerated women attending a prison school. During that project, she hired an assistant to transcribe audiotapes of interviews, participant observations, and field notes. In this paper, one context‐specific case is used to examine the complexities of transcription work involving a person other than the researcher. Lave and Wenger's (1991) “legitimate peripheral participation” serves as an analytical framework to explore the learning experienced by both researcher and transcriber as a result of their co‐participation in the project. Transcripts of four interviews conducted with the transcriber provide the basis for the investigation. The findings disrupt simplistic notions of the transcription process and show how peripheral participation can lead to educational experiences for those involved.
BIST Scheme Based on Reseeding ofMultiple Polynomial Linear Feedback Shift

In this paper we describe an optimized BIST scheme based on reseeding of multiple polynomial Linear Feedback Shift Registers (LFSRs). The same LFSR that is used to generate pseudo-random patterns, is loaded with seeds from which it produces vectors that cover the testcubes of dif-cult to test faults. The scheme is compatible with scan-design and achieves full coverage as it is based on random patterns combined with a deterministic test set. A method for processing the test set to allow for eecient encoding by the scheme is described. Algorithms for calculating LFSR seeds from the test set and for the selection and ordering of polynomials are described. Experimental results are provided for ISCAS-89 benchmark circuits to demonstrate the eeectiveness of the scheme. The scheme allows an excellent trade-oo between test data storage and test application time (number of test patterns) with a very small hardware overhead. We show the trade-oo between test data storage and number of test patterns under the scheme.