Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards development of OER derived custom-built open textbooks: A baseline survey of university teachers at the University of the South Pacific

Textbook prices have soared over the years, with several studies revealing many university students are finding it difficult to afford textbooks. Fortunately, two innovations – open educational resources (OER) and open textbooks – hold the potential to increase textbook affordability. Experts, though, have stated the obvious: that students can save money through open textbooks only if teachers are willing to develop and use them. Considering both the high price of textbooks and the benefits offered by OER and open textbooks, the aim of this study was to assess the University of the South Pacific (USP) teachers’ willingness towards development of custom-built OER derived open textbooks for their courses with a focus on providing a foundation for strategies to promote open textbook development at USP. This paper reports the findings of an online survey of 39 USP teachers. The results show that 17 teachers were willing to develop OER derived custom-built open textbooks for their courses. Besides this, there are findings relating to six important areas: teachers’ motivation to develop open textbooks; the frequency of more than one prescribed textbook per course; teachers’ awareness of the costs of the prescribed textbooks; the average cost of prescribed textbooks in a course; teachers’ awareness and utilization of OER and open textbooks; and teachers’ perceived barriers to using OER and types of challenges they encounter while using OER. These findings have been discussed in relation to research studies on OER and open textbooks.
High resolution slab gel electrophoresis of 8‐amino‐1,3,6‐pyrenetrisulfonic acid (APTS) tagged oligosaccharides using a DNA sequencer

A novel electrophoretic method for the analysis of oligosaccharides using DNA sequencer technology is illustrated using malto‐oligosaccharide distributions obtained following isoamylase disgestion of glycogen, wheat starch and potato starch. The debranched starches were derivatized at the reducing end with the charged fluorophore 8‐amino‐1,3,6‐pyrenetrisulfonic acid (APTS). This highly reproducible method provides baseline resolution of oligomers from chain lengths of 3 to more than 80 glucose units, and exhibits high sensitivity with detection thresholds of one femtomole per resolved band. In addition, the reductive amination procedure attaches a single fluorophore per oligosaccharide, allowing calculation of the results on either a mass or a molar basis. The efficacy of the method is illustrated through the determination of the profile of individual oligosaccharides of chain length with a degree of polymerization (DP) < 80, derived from loading less than 15 ng per analysis of glycogen, wheat and potato starches. While the results obtained were superior in resolution and sensitivity to previously reported observations using a range of techniques, they were nonetheless consistent with the overall differences between these polysaccharides. The resolution, sensitivity, reproducibility and high throughput of the method provides substantial advantages over existing methods for the analysis of linear oligosaccharide chain length distributions.
Possible involvement of α1-adrenergic receptor and KATP channels in cardioprotective effect of remote aortic preconditioning in isolated rat heart

Background: Remote preconditioning is a phenomenon in which brief episodes of ischemia and reperfusion to remote organs protect the target organ against sustained ischemia/reperfusion (I/R)-induced injury. Protective effects of remote aortic preconditioning (RAPC) are well established in the heart, but their mechanisms still remain to be elucidated. Objective: This study has been designed to investigate the possible involvement of α-1-adrenergic receptor (AR) and KATP channels in cardio-protective effect of RAPC in isolated rat heart. Materials and Methods: Four episodes of ischemia and reperfusion, each comprising of 5 min occlusion and 5 min reperfusion, were used to produce RAPC. Isolated perfused rat heart was subjected to global ischemia for 30 min followed by reperfusion for 120 min. Coronary effluent was analyzed for LDH and CK-MB release to assess the degree of cardiac injury. Myocardial infarct size was estimated macroscopically using TTC staining. Results: Phenylephrine (20 μ/kg i.p.), as α-1-AR agonist, was noted to produce RAPC-like cardio-protection. However, administration of glibenclamide concomitantly or prior to phenylephrine abolished cardioprotection. Moreover, prazocin (1 mg/kg. i.p), as α-1-AR antagonist and glibenclamide (1 mg/kg i.p), a KATP channel blocker, abolished the cardioprotective effect of RAPC. Conclusion: These data provide the evidence that α-1-AR activation involved in cardioprotective effect of RAPC-mediated trough opening of KATP channels.
Treatment of Chronic Obsessive-Compulsive Neurosis by in-vivo Exposure

Summary Twenty patients with chronic obsessive-compulsive rituals were treated in a partially controlled design by in-vivo (real life) exposure with self-imposed response prevention. Treatment included 4–12 weeks as in-patients, and lasted a mean of 23 sessions. All patients were followed-up for at least two years. No patients dropped out during the trial, though one refused domiciliary treatment after discharge. Significant improvement in compulsions was found after three weeks of real-life exposure, and continued during follow-up. At two years follow-up 14 patients were much improved, one improved and 5 unchanged; in a third year of follow-up the improved patient became symptom-free after further exposure treatment. Improvement after three weeks exposure predicted good outcome at 6 and 12 months follow-up. Muscular relaxation treatment had no significant effect on rituals. Modelling of exposure conferred no advantage over exposure alone for the group as a whole, though it may help selected patients. The role of response prevention is unknown. Patients' commitment to treatment facilitates exposure. Domiciliary treatment with involvement of family members in therapy seems crucial in some cases. Pilot group treatment of patients and families together suggests that this may be a useful adjuvant to individual treatment by increasing motivation and aiding follow-up. Compulsive slowness presents special treatment problems but can be improved by a prompting and pacing approach. The course of rituals was often independent of that of agoraphobia, marital problems and depression where these had initially coexisted with rituals. Depressive episodes were common before, during and after treatment, and required tricyclic medication. The trial sample was predominantly female but was otherwise typical of patients with compulsive rituals. Of the 125 obsessive-compulsives seen in the first author's unit over four years 96 per cent were offered behavioural or antidepressant treatment. One quarter refused behavioural treatment after it was offered. Real-life exposure with self-imposed response prevention is usually an effective procedure for lasting reduction of chronic compulsive rituals in well motivated patients.
What counts as knowledge: learning to use categories in computer environments

In this article, I develop a perspective on learning as multilayered phenomena. I take a socio-genetic approach in order to understand human activity and to show how categories are a fundamental part of learning in a specific type of institutional practice. In the empirical section, student dialogue is analysed in relation to a set of categories taken from scientific discourse. The analysis illustrates how categories in the progressive inquiry model could guide students towards a more systematic orientation to problem solving.
A Highly Conserved Residue in HIV-1 Nef Alpha Helix 2 Modulates Protein Expression

The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution at Nef residue 84. These findings highlight residue A84 as a major determinant of HIV-1 Nef expression. ABSTRACT Extensive genetic diversity is a defining characteristic of human immunodeficiency virus type 1 (HIV-1) and poses a significant barrier to the development of an effective vaccine. To better understand the impact of this genetic diversity on the HIV-1 pathogenic factor Nef, we compiled a panel of reference strains from the NIH Los Alamos HIV Database. Initial sequence analysis identified point mutations at Nef residues 13, 84, and 92 in subtype C reference strain C.BR92025 from Brazil. Functional analysis revealed impaired major histocompatibility complex class I and CD4 downregulation of strain C.BR92025 Nef, which corresponded to decreased protein expression. Metabolic labeling demonstrated that strain C.BR92025 Nef has a greater rate of protein turnover than subtype B reference strain B.JRFL that, on the basis of mutational analysis, is related to Nef residue A84. An alanine-to-valine substitution at position 84, located in alpha helix 2 of Nef, was sufficient to alter the rate of turnover of an otherwise highly expressed Nef protein. In conclusion, these findings highlight HIV-1 Nef residue A84 as a major determinant of protein expression that may offer an additional avenue to disrupt or mediate the effects of this key HIV-1 pathogenic factor. IMPORTANCE The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution at Nef residue 84. These findings highlight residue A84 as a major determinant of HIV-1 Nef expression.
How Enjoyable Was It? Remembering an Affective Reaction to a Previous Consumption Experience

Consumers use affective reactions from previous exposure to experiences in decision making. However, other affective reactions derived from postexperience information (i.e., advertising) may interfere with the retrieval of experience-based reactions. The results of three experiments show that when postexperience affective reactions interfere with the retrieval of an experience-based reaction, consumers use postexperience behavior as a proxy for their liking of the experience. The use of postexperience behavior occurs even when the behavior is nondiagnostic. The results also indicate that participants are not consciously aware of the interfering effect of postexperience affective reactions or of their reliance on postexperience behavior when constructing memory. (c) 2007 by JOURNAL OF CONSUMER RESEARCH, Inc.
Driver familiarity modeling for generating navigation directions

Current and future in-vehicle personal assistant systems stand to benefit from knowledge of the level of familiarity that the driver has with different parts of the current route. Such systems could use this information to adapt driving directions to be more succinct, understandable and personalized. However accumulating evidence of familiarity by direct experience alone could take many months and still be incomplete. Instead, we propose building predictive models of driver familiarity with road networks by generalizing intelligently from a small sample of data. Inspired by psychology studies that suggest a variety of cognitive models of route familiarity in humans, we present an ensemble of familiarity models using different machine learning methods on GPS time series data collected during normal driving by a volunteer pool of 22 drivers from San Francisco Bay area. We validate the models' predictions through an extensive questionnaire administered to the subjects about route familiarity and need for directions along select routes. Our results indicate that a significant component of driver familiarity can be predicted from unobtrusively collected driving data. We conclude with a proposed approach for integrating such models with a generator of driving directions.
High repetition rate collisional soft X-ray lasers based on grazing incidence pumping

We discuss the demonstration of gain-saturated high repetition rate table-top soft X-ray lasers producing microwatt average powers at wavelengths ranging from 13.9 to 33 nm. The results were obtained heating a precreated plasma with a picosecond optical laser pulse impinging at grazing incidence onto a precreated plasma. This pumping geometry increases the energy deposition efficiency of the pump beam into the gain region, making it possible to saturate soft X-ray lasers in this wavelength range with a short pulse pump energy of only 1 J at 800-nm wavelength. Results corresponding to 5-Hz repetition rate operation of gain-saturated 14.7-nm Ni-like Pd and 32.6-nm line Ne-like Ti lasers pumped by a table-top Ti:sapphire laser are reported. We also discuss results obtained using a 1 /spl omega/1054-nm prepulse and 2 /spl omega/527-nm short pulse from a Nd:glass pump laser. This work demonstrates the feasibility of producing compact high average power soft X-ray lasers for applications.
Malnutrition among under-five children in India and strategies for control

Malnutrition among under-five children is an important concern for the health authorities in India. The aim of the present review was to assess the burden of under-nutrition and over-nutrition, its determinants and strategies required to tackle malnutrition among under-five children in India. Recent data were collected from Google search, Medline, and others. The information retrieved was reviewed and analyzed for discrepancies. Existing evidence shows that the prevalence of under-nutrition among under-five children was high and varied widely (under-weight: 39-75%, stunting: 15.4-74%, wasting: 10.6-42.3%) depending on the assessment methodology adopted. Studies on assessment of over-nutrition status among under-five children were limited. Distribution of various types of risk factors and its influence on nutrition status of children in a given set up should be analyzed for planning the control measures. Strengthening public health interventions for mild malnutrition cases and vulnerable groups, effective implementation and evaluation of the strategies at regional level, research on overweight, obesity and its etiological factors and steps for improving socioeconomic development are the prerequisites for tackling malnutrition among under-five children in India.
Web Directories as Training Data for Automated Metadata Extraction

Although man-made annotations are considered as the main ‘knowledge fuel’ for the Semantic Web, the majority of existing commercial pages are still poorly equipped with any kind of metadata, never mind the forthcoming standards such as the RDF syntax or the Dublin Core semantics. Information Extraction, relying on characteristic patterns in text, can be applied even on such ‘legacy’ pages, in order to obtain metadata containing, for example, the names, types, and domains of activity of the WWW subjects (companies).
REVIEW OF MEASUREMENT ITEM OF ENGINEERING STUDENTS’ LEARNING ENVIRONMENT: CONFIRMATORY FACTOR ANALYSIS

This survey study was carried out to review the measurement items of learning environment model for engineering students. A total of 535 respondents were involved in this research. The variables presented in this research were the peer interaction, lecturer interaction and education facilities. Data were analyzed descriptively for reliability (Cronbach Alpha values) and confirmatory factor analysis (CFA) was used to obtain 3 factor solutions using AMOS software. The results showed that the Cronbach Alpha was on the classification of high and very high which was higher than 0.70. Result of CFA confirmed 3 factors solution with data collected was fit with model. The study also proposed a model of learning environment for engineering students.
Diagnosis of epithelial mesothelioma using tree‐based regression analysis and a minimal panel of antibodies

Aims: Immunohistochemistry with panels of antibodies is a standard procedure to distinguish between malignant mesothelioma and metastatic adenocarcinoma. Most studies assess only the sensitivity and specificity for single antibodies, even when the paper concludes by recommending an antibody panel. It was the aim of this study to use a novel statistical approach to identify a minimal panel of antibodies, which would make this distinction in the majority of cases. Methods: Two hundred consecutive cases of pleural malignancy (173 pleural mesotheliomas of epithelial type and 27 cases of secondary adenocarcinoma) were investigated using a standard panel of 12 antibodies (CAM5.2, CK5/6, calretinin, HBME‐1, thrombomodulin, WT‐1, EMA, CEA, CD15, B72.3, BG8, and TTF‐1). Regression and classification tree‐based methods were applied to select the best combination of markers. The modelling procedures used employ successive, hierarchical predictions computed for individual cases to sort them into homogeneous classes. Results: Labelling for calretinin and lack of labelling for BG8 were sufficient for definite correlation with a diagnosis of malignant mesothelioma. CD15 provided further differentiating information in some cases. Conclusion: A panel of three antibodies was sufficient in most cases to diagnose, or to exclude, epithelial mesothelioma. Calretinin exhibits the strongest correlative power of the antibodies tested.
Constructing a Chinese International Relations Theory: A Sociological Approach to Intellectual Innovation

Chinese scholars are debating whether, and how, to innovate a Chinese theory of International Relations (IR). This article examines the driving forces behind this theoretical debate. It challenges the commonsensical link between external events in the subject matter (i.r.) and theorizing (IR), which suggests that the innovation of a Chinese IR theory is a natural product of China's geopolitical rise, its growing political ambitions, and discontent with Western hegemony. We propose instead a sociological approach to intellectual innovation which opens the black box of knowledge production, and argue that theoretical innovation, in China and elsewhere, is best understood as an interplay between internal and external layers. The internal academic context comprises intellectuals pursuing prominence, with each intellectual trying to carve out a maximally distinct position in order to receive attention from their peers—theorizing a Chinese IR theory being one important way of doing this. The external layer—which ranges from power politics to sociopolitical developments—affects this process indirectly by providing more research funds and autonomy to the more immediate institutional environment where control over rewards such as research funds, promotion, and publications affects what kind of work is done, with theorizing being increasingly rewarded.
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification

Gene function curation of the literature with Gene Ontology (GO) concepts is one particularly time-consuming task in genomics, and the help from bioinformatics is highly requested to keep up with the flow of publications. In 2004, the first BioCreative challenge already designed a task of automatic GO concepts assignment from a full text. At this time, results were judged far from reaching the performances required by real curation workflows. In particular, supervised approaches produced the most disappointing results because of lack of training data. Ten years later, the available curation data have massively grown. In 2013, the BioCreative IV GO task revisited the automatic GO assignment task. For this issue, we investigated the power of our supervised classifier, GOCat. GOCat computes similarities between an input text and already curated instances contained in a knowledge base to infer GO concepts. The subtask A consisted in selecting GO evidence sentences for a relevant gene in a full text. For this, we designed a state-of-the-art supervised statistical approach, using a naïve Bayes classifier and the official training set, and obtained fair results. The subtask B consisted in predicting GO concepts from the previous output. For this, we applied GOCat and reached leading results, up to 65% for hierarchical recall in the top 20 outputted concepts. Contrary to previous competitions, machine learning has this time outperformed standard dictionary-based approaches. Thanks to BioCreative IV, we were able to design a complete workflow for curation: given a gene name and a full text, this system is able to select evidence sentences for curation and to deliver highly relevant GO concepts. Contrary to previous competitions, machine learning this time outperformed dictionary-based systems. Observed performances are sufficient for being used in a real semiautomatic curation workflow. GOCat is available at http://eagl.unige. ch/GOCat/. Database URL: http://eagl.unige. ch/GOCat4FT/
A comprehensive simulation study on classification of RNA-Seq data

RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of gene-expression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption. Hence, these methods cannot be directly applied to RNA-Seq data since they violate both data structure and distributional assumptions. However, it is possible to apply these algorithms with appropriate modifications to RNA-Seq data. One way is to develop count-based classifiers, such as Poisson linear discriminant analysis and negative binomial linear discriminant analysis. Another way is to bring the data closer to microarrays and apply microarray-based classifiers. In this study, we compared several classifiers including PLDA with and without power transformation, NBLDA, single SVM, bagging SVM (bagSVM), classification and regression trees (CART), and random forests (RF). We also examined the effect of several parameters such as overdispersion, sample size, number of genes, number of classes, differential-expression rate, and the transformation method on model performances. A comprehensive simulation study is conducted and the results are compared with the results of two miRNA and two mRNA experimental datasets. The results revealed that increasing the sample size, differential-expression rate and decreasing the dispersion parameter and number of groups lead to an increase in classification accuracy. Similar with differential-expression studies, the classification of RNA-Seq data requires careful attention when handling data overdispersion. We conclude that, as a count-based classifier, the power transformed PLDA and, as a microarray-based classifier, vst or rlog transformed RF and SVM classifiers may be a good choice for classification. An R/BIOCONDUCTOR package, MLSeq, is freely available at https://www.bioconductor. org/packages/release/bioc/html/MLSeq.html.