Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Basis for the Substrate Specificity of Tobacco Etch Virus Protease*

Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-Å resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.
Teaching writing to low proficiency EFL students

This article describes a genre-based literacy pedagogy which can be used with English language learners. The pedagogy discussed involves a combination of two explicit teaching methodologies, a genre-based and activity-based pedagogical approach. The pedagogy was introduced in an English Club at a local Hong Kong school, as part of a collaborative research project. In this article, we discuss the approach used and present examples of the students' work. The findings are particularly suitable for educational contexts where the students are low proficiency English as a foreign language (EFL) learners.
Young children's phonological awareness and nonword repetition as a function of vocabulary development.

The role of vocabulary growth in the development of two reading-related phonological processes was examined. In Experiments I and 2, 4- and 5-year-olds and a sample of first graders performed better on phonological awareness tasks for word versus pseudoword stimuli, and for highly familiar versus less familiar words. Three- and 4-year-olds in Experiment 3 performed better for words with many versus few similarly sounding items in a listener's lexicon. Vocabulary was strongly associated with nonword repetition scores for 3- to 5-year olds. The shared variance of this association was accounted for by phonological awareness measures and did not appear to be due to phonological short-term memory, as previously argued. The author proposes that vocabulary growth, defined in terms of absolute size, word familiarity, and phonological similarity relations between word items, helps to explain individual differences in emerging phonological awareness and nonword repetition.
Assessing Sensitivity to an Unobserved Binary Covariate in a Nonrandomized Experiment with Binary Outcome.

Abstract : The results of nonrandomized clinical experiments are often disputed because patients at greater risk may be overrepresented in some treatment groups. This paper proposes a simple technique providing insight into the range of plausible conclusions from a nonrandomized experiment with binary outcome and observed categorical covariate. The technique assesses the sensitivity of conclusions to assumptions about an unobserved binary covariate relevant to treatment assignment, and is illustrated in a medical study of coronary artery disease. (Author)
A review of a decade’s scholarly publications (2004–2013) in the South African Journal of Industrial Psychology

Orientation: Publishing methodologically sound, empirically based studies in reputable accredited scientific journals are essential in order to advance knowledge and evidence-based practice in the field of industrial and organisational psychology. Research purpose: The purpose of the research was to conduct a broad content analysis of the articles published in the South African Journal of Industrial Psychology (SAJIP) between 2004 and 2013. The study aimed to provide a descriptive overview of the most frequent content themes,published authors and institutions, research approaches, strategies, designs and analysis techniques, software packages and sample sizes in industrial and organisational (I-O) psychology utilised in the publications. Motivation for study: The periodic analyses of published content in scholarly journals provide an index of the extent to which the publications reflect the scope of practice in a given discipline and broaden insight into the direction and relevance of research published in a journal. Research design, approach and method: A broad systematic content analysis was conducted of 342 documented articles published in the SAJIP between 2004 and 2013. Descriptive data(frequencies and percentages) were used to report the findings. Main findings: The publishing pattern of the SAJIP appeared to correspond with its focus and scope. Manuscripts utilising mostly cross-sectional quantitative correlational research designs with large samples ( n > 201) were published in the SAJIP. The University of Johannesburg and Professor Sebastiaan (Ian) Rothmann were the largest contributors to publications between 2004 and 2013. Organisational psychology and psychometrics were the most prominent domains in I-O psychology research. Data were predominantly processed utilising SPSS. Practical implications: The insights derived from the findings can be employed to plan future research initiatives in the field of I-O psychology. Contribution/value-add: The findings provide valuable insight into the current status of the foci of I-O psychology research as published in the SAJIP between 2004 and 2013 and the contribution made by the SAJIP to advancing knowledge and evidence-based practice in I-O psychology.
Psychiatric morbidity and socio-occupational dysfunction in residents of a drug rehabilitation centre: challenges of substance misuse management in a Bruneian context†

Aims and method In 2011, a psychiatric clinic was started in Pusat Al-Islah, a drug rehabilitation centre. Our aim was to record self-reported socio-occupational dysfunction and patterns of drug misuse and to evaluate the usefulness of a psychiatric screening tool. A two-phased approach using the Self-Reporting Questionnaire (SRQ) and the Mini International Neuropsychiatric Interview (MINI) was used to examine the rates of psychiatric diagnoses. Results Methamphetamine was the most commonly misused substance in 94.5% of residents. High levels of socio-occupational dysfunction were reported. In total, 5.5% met criteria for major depressive disorder, 4.8% for lifetime psychotic disorder and 11.5% for suicidal ideation. In addition, 13.3% reported previous untreated mental health problems. Clinical implications A screening tool such as the SRQ can be used to identify those needing further psychiatric assessment. Interventions to address amphetamine misuse and associated socio-occupational dysfunction are required. Societal views and legislation influence the management of substance misuse problems in Brunei.
Olfactory Dysfunction in Multiple Sclerosis: Evidence of a Decrease in Different Aspects of Olfactory Function

Background/Aims: Numerous authors have described olfactory dysfunction in multiple sclerosis (MS) in recent years. The aim of this study was to specify the aspects of olfactory perception that are most affected and to identify any correlations with clinical, anatomical and functional data. Methods: 50 patients with remitting or secondary progressive MS were included. Personal data were collected (medical history, characteristics of their disease, depression and disability scores and number of lesions on cerebral imaging). An olfactory test (Sniffin Sticks®) was used to evaluate subjects’ olfactory function. Results: The odor detection threshold is the most sensitive marker, with 40% of patients presenting hyposmia. The ability to identify odors is affected later on, and is inversely correlated with the level of disability. Conclusion: Our results confirm that several aspects of olfactory function are altered in MS, particularly those aspects requiring greater cognitive involvement, such as discrimination and identification of odors.
Improved Working Memory but No Effect on Striatal Vesicular Monoamine Transporter Type 2 after Omega-3 Polyunsaturated Fatty Acid Supplementation

Studies in rodents indicate that diets deficient in omega-3 polyunsaturated fatty acids (n–3 PUFA) lower dopamine neurotransmission as measured by striatal vesicular monoamine transporter type 2 (VMAT2) density and amphetamine-induced dopamine release. This suggests that dietary supplementation with fish oil might increase VMAT2 availability, enhance dopamine storage and release, and improve dopamine-dependent cognitive functions such as working memory. To investigate this mechanism in humans, positron emission tomography (PET) was used to measure VMAT2 availability pre- and post-supplementation of n–3 PUFA in healthy individuals. Healthy young adult subjects were scanned with PET using [11C]-(+)-α-dihydrotetrabenzine (DTBZ) before and after six months of n–3 PUFA supplementation (Lovaza, 2 g/day containing docosahexaenonic acid, DHA 750 mg/d and eicosapentaenoic acid, EPA 930 mg/d). In addition, subjects underwent a working memory task (n-back) and red blood cell membrane (RBC) fatty acid composition analysis pre- and post-supplementation. RBC analysis showed a significant increase in both DHA and EPA post-supplementation. In contrast, no significant change in [11C]DTBZ binding potential (BPND) in striatum and its subdivisions were observed after supplementation with n–3 PUFA. No correlation was evident between n–3 PUFA induced change in RBC DHA or EPA levels and change in [11C]DTBZ BPND in striatal subdivisions. However, pre-supplementation RBC DHA levels was predictive of baseline performance (i.e., adjusted hit rate, AHR on 3-back) on the n-back task (y = 0.19+0.07, r2 = 0.55, p = 0.009). In addition, subjects AHR performance improved on 3-back post-supplementation (pre 0.65±0.27, post 0.80±0.15, p = 0.04). The correlation between n-back performance, and DHA levels are consistent with reports in which higher DHA levels is related to improved cognitive performance. However, the lack of change in [11C]DBTZ BPND indicates that striatal VMAT2 regulation is not the mechanism of action by which n–3 PUFA improves cognitive performance.
Making Ways for Change: Museums, Disruptive Technologies and Organisational Change

Abstract This paper aims to stimulate discussion about the nature of technology-related organisational change and how it is managed within museums. It argues that how we think about and understand change affects our ability to anticipate, shape and direct it. Drawing upon perspectives from sociology, information systems, management and organisation theory, this paper explores how we might understand and better manage change within the museums sector generally and, in particular, that which arises in our use of digital information and communication technologies (ICTs). It advocates the conscious use of theory, particularly organisational theory, to encourage new perspectives on organisations and the challenge of change represented by technology. Organisational theory particularly that informed by the ‘new science’ of complexity provides a rich source of insights about the nature of change which have so far been lacking in the discussion of digital cultural heritage within museums.
Word Recognition in Arabic as a Foreign Language

This study is an empirical investigation of the impact ol the Arabic writing system in Arabic as a foreign language (AFL) learners' visual word recognition. The study investigates the effect of unfamiliar graphemes and phonemes, whether the missing vowels inhibit reading speed and comprehension and whether learners are able to apply the system of root and pattern in Semitic morphology to compensate for the lack of vowel information. Participants are 71 learners of Arabic at 3 different proficiency levels and a control group of 24 native speakers. Results indicate that the Arabic writing system represents a major obstacle to the establishment of automatic word recognition, which is a prerequisite for "skilled reading": Although both pseudoword decoding and text reading improves remarkably from the beginning to intermediate level, progression then stalls. Based on these results, extended and more explicit training of decoding skills in AFL teaching is recommended. [ABSTRACT FROM AUTHOR]
SH2 Ligand-Like Effects of Second Cytosolic Domain of Na/K-ATPase α1 Subunit on Src Kinase

Our previous studies have suggested that the α1 Na/K-ATPase interacts with Src to form a receptor complex. In vitro binding assays indicate an interaction between second cytosolic domain (CD2) of Na/K-ATPase α1 subunit and Src SH2 domain. Since SH2 domain targets Src to specific signaling complexes, we expressed CD2 as a cytosolic protein and studied whether it could act as a Src SH2 ligand in LLC-PK1 cells. Co-immunoprecipitation analyses indicated a direct binding of CD2 to Src, consistent with the in vitro binding data. Functionally, CD2 expression increased basal Src activity, suggesting a Src SH2 ligand-like property of CD2. Consistently, we found that CD2 expression attenuated several signaling pathways where Src plays an important role. For instance, although it increased surface expression of Na/K-ATPase, it decreased ouabain-induced activation of Src and ERK by blocking the formation of Na/K-ATPase/Src complex. Moreover, it also attenuated cell attachment-induced activation of Src/FAK. Consequently, CD2 delayed cell spreading, and inhibited cell proliferation. Furthermore, these effects appear to be Src-specific because CD2 expression had no effect on EGF-induced activation of EGF receptor and ERK. Hence, the new findings indicate the importance of Na/K-ATPase/Src interaction in ouabain-induced signal transduction, and support the proposition that the CD2 peptide may be utilized as a Src SH2 ligand capable of blocking Src-dependent signaling pathways via a different mechanism from a general Src kinase inhibitor.
Discovery of New Cargo Proteins that Enter Cells through Clathrin‐Independent Endocytosis

Clathrin‐independent endocytosis (CIE) allows internalization of plasma membrane proteins lacking clathrin‐targeting sequences, such as the major histocompatibility complex class I protein (MHCI), into cells. After internalization, vesicles containing MHCI fuse with transferrin‐containing endosomes generated from clathrin‐dependent endocytosis. In HeLa cells, MHCI is subsequently routed to late endosomes or recycled back out to the plasma membrane (PM) in distinctive tubular carriers. Arf6 is associated with endosomal membranes carrying CIE cargo and expression of an active form of Arf6 leads to the generation of vacuolar structures that trap CIE cargo immediately after endocytosis, blocking the convergence with transferrin‐containing endosomes. We isolated these trapped vacuolar structures and analyzed their protein composition by mass spectrometry. Here we identify and validate six new endogenous cargo proteins (CD44, CD55, CD98, CD147, Glut1, and ICAM1) that use CIE to enter cells. CD55 and Glut1 appear to closely parallel the trafficking of MHCI, merging with transferrin endosomes before entering the recycling tubules. In contrast, CD44, CD98, and CD147 appear to directly enter the recycling tubules and by‐pass the merge with EEA1‐positive, transferrin‐containing endosomes. This divergent itinerary suggests that sorting may occur along this CIE pathway. Furthermore, the identification of new cargo proteins will assist others studying CIE in different cell types and tissues.
Emotional intelligence and self-efficacy as determinants of academic achievement in English language among students in Oyo state senior secondary schools

This study investigated the impact of emotional intelligence and self efficacy training on academic achievement in English Language of students in Senior Secondary Schools. The sample consisted of 270 participants drawn from nine co-educational schools across three selected educational zones. Simple random sampling technique was used to select three schools from each zone among those that met the inclusion criteria set for the study. Adopting a pre-test, post-test, control group quasi-experiile mental design, one null hypothesis was tested at 0.05 level of significance. Using Emotional Intelligence Training Package (EIPTA), Self Efficacy Training Package (SEPTA) and English Language Achievement Test (r=0.73), the administration of interventions lasted for eight weeks. Data were analysed using ANCOVA and the Duncan post hoc test to examine the impact of emotional intelligence and self efficacy training on the achievement of senior secondary school students in English language.
Prediction of carboplatin clearance from standard morphological and biological patient characteristics.

BACKGROUND Hematologic toxicity of an antineoplastic drug, carboplatin, is largely dependent on its pharmacokinetics. Its therapeutic efficacy may be related to plasma drug exposure. Dosage adjustment based on isotopic determination of glomerular filtration rate has been proposed, but its ambulatory use is not yet conceivable. The dosage adjustment based on a patient's creatinine clearance relies on accurate measurement of urine volume per unit time and can be done with ease. PURPOSE A population pharmacokinetics study was undertaken to determine a relationship between carboplatin clearance and patient characteristics. A predictive formula was derived that was then prospectively evaluated, and its outcome was compared with that obtained by other methods available to predict carboplatin clearance. METHODS Plasma carboplatin pharmacokinetics determined as ultrafilterable platinum in 70 patients (age range, 23-84 years) treated with different combination regimens that included carboplatin at doses ranging from 184 mg to 950 mg (1-hour intravenous infusion) for various tumor types. Data were analyzed using the nonlinear mixed effects model (NONMEM). The data from 34 patients (46 cycles) were utilized to derive the most predictive formula. The reliability of the formula was subsequently evaluated by analyzing the data obtained from 36 other patients (49 cycles). RESULTS Carboplatin clearance (mL/min) was found to be best predicted by the following formula: 0.134. weight + [218.weight. (1-0.00457.age). (1-0.314.sex)]creatinine expressed in micromolar concentration (with weight in kg, age in years, and sex = 0 if male and sex = 1 if female). Prospectively, this formula predicted the carboplatin clearance with good precision (median absolute percent error of 10% [range, 0% to 30%]) and minimal bias (median percent error of 2% [range, -25% to 30%]). This method of prediction was as accurate as the one derived from the measurement of glomerular filtration rate following the injection of 51 chromium-EDTA. CONCLUSION This formula for the determination of carboplatin clearance can permit individualized determination of carboplatin dosage in adults by simply multiplying the calculated carboplatin clearance by the area under the curve for the desired dosage administration.
Small Sample Confidence Intervals for Multivariate Impulse Response Functions at Long Horizons

Existing methods for constructing confidence bands for multivariate impulse response functions depend on auxiliary assumptions on the order of integration of the variables. Thus, they may have poor coverage at long lead times when variables are highly persistent. Solutions that have been proposed in the literature may be computationally challenging. The goal of this paper is to propose a simple method for constructing confidence bands for impulse response functions that are robust to the presence of highly persistent processes. We do so by using alternative approximations based on local-to-unity asymptotic theory and by allowing the lead time of the impulse response function to be a fixed fraction of the sample size. Monte Carlo simulations, in which this method is compared with those existing in the literature, show that our method has good coverage properties. We also investigate the properties of the various methods in terms of the length of their confidence bands. Finally, we show, with empirical applications, that our method may provide different economic interpretations of the data. An example to the analysis of nominal versus real sources of fluctuations in real and nominal exchange rates is discussed
Old Wine In New Bottles? Researching Effective Schools in Developing Countries

This article looks at the current state of play in research into effective schools in the developing world and seeks to identify some of the underlying concerns arising from this work. School effectiveness research in developing countries will be contrasted with that within the developed world, and will be analysed in the context of the work of donor agencies and of the demands made by structural adjustment policies. A view of 'school effectiveness' which is contextually-related is posited, stressing the need to examine whether an examination of the effectiveness of schools should be considered in terms of the perceptions of different stakeholders, rather than in relation to an 'objective' checklist derived from research in a different cultural context, and often done years earlier.
When lives are put on hold: Lengthy asylum processes decrease employment among refugees

Refugees waiting an additional year for their asylum claim decision face a 20% reduction in their subsequent employment rate. European governments are struggling with the biggest refugee crisis since World War II, but there exists little evidence regarding how the management of the asylum process affects the subsequent integration of refugees in the host country. We provide new causal evidence about how one central policy parameter, the length of time that refugees wait in limbo for a decision on their asylum claim, affects their subsequent economic integration. Exploiting exogenous variation in wait times and registry panel data covering refugees who applied in Switzerland between 1994 and 2004, we find that one additional year of waiting reduces the subsequent employment rate by 4 to 5 percentage points, a 16 to 23% drop compared to the average rate. This deleterious effect is remarkably stable across different subgroups of refugees stratified by gender, origin, age at arrival, and assigned language region, a pattern consistent with the idea that waiting in limbo dampens refugee employment through psychological discouragement, rather than a skill atrophy mechanism. Overall, our results suggest that marginally reducing the asylum waiting period can help reduce public expenditures and unlock the economic potential of refugees by increasing employment among this vulnerable population.
Antimicrobial Activity, Growth Inhibition of Human Tumour Cell Lines, and Phytochemical Characterization of the Hydromethanolic Extract Obtained from Sapindus saponaria L. Aerial Parts

The hydromethanolic extract of Sapindus saponaria L. aerial parts was investigated for antimicrobial activity (against several Gram-positive and Gram-negative bacteria and fungi) and capacity to inhibit the growth of different human tumor cell lines as also nontumor liver cells. The evaluated extract was further characterized in terms of phytochemicals using UV, 1H-NMR, 13C-NMR, and MS spectroscopic tools. The extract has shown a significant antimicrobial activity on all tested bacterial and fungal species. The best activity was achieved against Bacillus cereus and Staphylococcus aureus among bacteria and against all three Penicillium species tested. It also revealed cytotoxicity against human colon (HCT-15), cervical (HeLa), breast (MCF-7), and lung (NCI-H460) carcinoma cell lines, with HeLa being the most susceptible tumor cell line. The extract was not toxic for nontumor liver cells. Chromatographic separation of the extract resulted in the isolation and identification of stigmasterol, oleanolic acid, luteolin, luteolin 8-C-β-glucoside (orientin), luteolin 6-C-β-glucoside (isoorientin), luteolin 7-O-β-glucuronide, and rutin. The results of the present findings may be useful for the discovery of novel antitumor and antimicrobial agents from plant origin.