Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias

The tRNA adaptation index (tAI) is a widely used measure of the efficiency by which a coding sequence is recognized by the intra-cellular tRNA pool. This index includes among others weights that represent wobble interactions between codons and tRNA molecules. Currently, these weights are based only on the gene expression in Saccharomyces cerevisiae. However, the efficiencies of the different codon–tRNA interactions are expected to vary among different organisms. In this study, we suggest a new approach for adjusting the tAI weights to any target model organism without the need for gene expression measurements. Our method is based on optimizing the correlation between the tAI and a measure of codon usage bias. Here, we show that in non-fungal the new tAI weights predict protein abundance significantly better than the traditional tAI weights. The unique tRNA–codon adaptation weights computed for 100 different organisms exhibit a significant correlation with evolutionary distance. The reported results demonstrate the usefulness of the new measure in future genomic studies.
Withaferin A inhibits experimental epithelial–mesenchymal transition in MCF‐10A cells and suppresses vimentin protein level in vivo in breast tumors

We have shown previously that withaferin A (WA), a bioactive component of the medicinal plant Withania somnifera, inhibits growth of cultured and xenografted human breast cancer cells and prevents breast cancer development and pulmonary metastasis incidence in a transgenic mouse model. The present study was undertaken to determine if the anticancer effect of WA involved inhibition of epithelial–mesenchymal transition (EMT). Experimental EMT induced by exposure of MCF‐10A cells to tumor necrosis factor‐α (TNF‐α) and transforming growth factor‐β1 (TGF‐β) was partially reversed by treatment with WA but not by its structural analogs withanone or withanolide A. Combined TNF‐α and TGF‐β treatments conferred partial protection against MCF‐10A cell migration inhibition by WA. Inhibition of TNF‐α and TGF‐β‐induced MCF‐10A cell migration by WA exposure was modestly attenuated by knockdown of E‐cadherin protein. MCF‐7 and MDA‐MB‐231 cells exposed to WA exhibited sustained (MCF‐7) or transient (MDA‐MB‐231) induction of E‐cadherin protein. On the other hand, the level of vimentin protein was increased markedly after 24 h treatment of MDA‐MB‐231 cells with WA. WA‐induced apoptosis was not affected by vimentin protein knockdown in MDA‐MB‐231 cells. Protein level of vimentin was significantly lower in the MDA‐MB‐231 xenografts as well as in MMTV‐neu tumors from WA‐treated mice compared with controls. The major conclusions of the present study are that (a) WA treatment inhibits experimental EMT in MCF‐10A cells, and (b) mammary cancer growth inhibition by WA administration is associated with suppression of vimentin protein expression in vivo. © 2013 Wiley Periodicals, Inc.
Welcoming the stranger: a qualitative analysis of teachers' views regarding the integration of refugee pupils into schools in Newcastle upon Tyne

The arrival of refugee pupils in UK schools has presented significant challenges to staff, pupils and families. The aim of this study was to record and analyse the views of teaching staff regarding their experiences of integrating these pupils into schools in Newcastle upon Tyne. A questionnaire was sent to 53 schools in the city known to have pupils who are refugees or asylum seekers. Questions focused on key issues identified by the Local Education Authority Working Group for Refugees and Asylum Seekers, including the dissemination of information prior to the arrival of new pupils, staff training and the response of the school community as a whole. Twenty‐four questionnaires were completed (response rate 45.3%), from two nurseries, 13 primary schools, seven secondary schools and one special school. The overwhelming need identified was for improved access to interpreting services, and more reliable information about pupils’ backgrounds. It was evident that integration is approached differently by individual schools depending on their overall ethnic mix and the availability of resources and support networks.
Effect of drought on safflower natural dyes and their biological activities

Drought is the main abiotic constraint that affects crop species behaviour regarding bio-chemical responses. The current study was conducted to examine the effect of water deficit on growth, phenolic and carotenoid contents as well as the antioxidant and antimicrobial activities of two Carthamus tinctorius varieties (Jawhara and 104) flowers. Hence, plants were treated with different levels of water deficit: control (100 %), moderate water deficit (50 %) and severe water deficit (25 %). Obtained results showed that plant growth was significantly (p < 0.05) reduced under 50 %. Drought increased flower phenolic acids contents especially gallic acid where they increased significantly (p < 0.05) by 2.73 fold (104) and by 2.87 fold (Jawhara) with respect to controls under 50 %. However, the amounts of this major compound were reduced at 25 % by 9.66 % (104) and 3.83 % (Jawhara). Similar to phenolic compounds, total carotenoid content was at its highest level especially for Jawhara with an increase by 35.19 % at 50 %. On the other hands, C. tinctorius flowers extracts exhibited high antiradical activity as compared to BHT. A gradual increase by 35.29 % (Jawhara) and 33.33 % (104) especially under 25 % was observed. Moreover, under 50 %, the antimicrobial activity increased significantly (p < 0.05) by 30 % and 10.05 % against Aspergillus carbonarus and Pseudomonas aerogenosa, respectively. Taken together, our findings suggest that C. tinctorius could be a raw material for production of natural dyes under moderate salinity conditions.
Being a Deaf Role Model: Deaf People's Experiences of Working with Families and Deaf Young People

Abstract The experiences of being a deaf role model have been little explored in the literature. This paper explores the role of the deaf role model as perceived by d/Deaf adults who carried out this role, when working with deaf young people, parents of deaf children, and professionals who work with them. The data were collected from part of the evaluation study of the National Deaf Children's Society's deaf role model project. Five focus groups were carried out with d/Deaf adults who were trained to be deaf role models across the UK. From deaf role models' perspective, five key issues were identified: the value of training; perceived benefits for families/deaf young people; managing parental expectations; addressing parental attitudes to deafness; and the personal impact of being a deaf role model. Recognizing and valuing d/Deaf adults' work with the families of deaf children/young people will benefit not only families and the other professionals who work with them, but also d/Deaf adults themselves.
Alveolar hemorrhage in systemic lupus erythematosus: a cohort review

Diffuse alveolar hemorrhage (DAH) is a rare but potentially catastrophic manifestation with a high mortality. Among rheumatologic diseases, it occurs most frequently in patients with systemic lupus erythematosus (SLE) and systemic vasculitis. Despite new diagnostic tools and therapies, it remains a diagnostic and therapeutic challenge. The aim of this work was to characterize the SLE patients with an episode of alveolar hemorrhage followed in our Clinical Immunology Unit (CIU). A retrospective chart review was carried out for all patients with SLE followed in CIU between 1984 and the end of 2013. We reviewed the following data: demographic characteristics, clinical and laboratory data, radiologic investigations, histologic studies, treatment, and outcome. We identified 10 episodes of DAH, corresponding to seven patients, all female. These represent 1.6% of SLE patients followed in our Unit. The age at DAH attack was 42.75 ± 18.9 years. The average time between diagnosis of SLE and the onset of DAH was 7.1 years. Three patients had the diagnosis of SLE and the DAH attack at the same time. Disease activity according to SLEDAI was high, ranging from 15 to 41. All patients were treated with methylprednisolone, 37.5% cyclophosphamide and 28.6% plasmapheresis. The overall mortality rate was 28.6%.
Reversal of acid‐induced and inflammatory pain by the selective ASIC3 inhibitor, APETx2

BACKGROUND AND PURPOSE Inflammatory pain is triggered by activation of pathways leading to the release of mediators such as bradykinin, prostaglandins, interleukins, ATP, growth factors and protons that sensitize peripheral nociceptors. The activation of acid‐sensitive ion channels (ASICs) may have particular relevance in the development and maintenance of inflammatory pain. ASIC3 is of particular interest due to its restricted tissue distribution in the nociceptive primary afferent fibres and its high sensitivity to protons.
Symbolic associations in neural network activations: Representations in the emergence of communication

Representation has a fundamental role in Artificial Intelligence but there is still an open debate on basic issues on this subject. Particularly, there have been various studies on the emergence of communication and language in artificial agents, where the debate on representations underlying these processes should be significant, however not much discussion and studies have been done. We propose to identify and classify possible representational processes occurring during the emergence of communication, replicating a computational experiment previously proposed and evaluating neural network activations patterns. To define representation and its classes, including icons, indexes and symbols, we rely on the semiotics of Charles Sanders Peirce. Results show that symbolic associations are established during the evolution of artificial agents and such symbolic associations benefit adaptive success.
Wait Times for Cancer Surgery in the United States: Trends and Predictors of Delays

Background:Patients frequently voice concerns regarding wait times for cancer treatment; however, little is known about the length of wait times from diagnosis to surgery in the United States. Our objectives were (1) to assess changes in wait times over the past decade and (2) to identify patient, tumor, and hospital factors associated with prolonged wait times for initial cancer treatment. Methods:Using the National Cancer Data Base (1995–2005), 1,228,071 patients were identified who underwent resection for nonmetastatic breast, colon, esophageal, gastric, liver, lung, pancreatic, and rectal cancer at 1443 hospitals. Multivariable models were developed to assess factors associated with time to treatment. Results:From 1995 to 2005, the median time from diagnosis to treatment increased for all cancers (P < 0.0001). The time from diagnosis to treatment was significantly longer at National Cancer Institute Comprehensive Cancer Centers and Veterans' Administration institutions versus community hospitals (P < 0.0001). On multivariable analysis, patients were significantly more likely to undergo initial treatment > 30 days from diagnosis if older (6 of 8 cancers), black (5 of 8 cancers), had more comorbidities (6 of 8 cancers), had Stage I disease (7 of 8 cancers), or were treated at National Cancer Institute Comprehensive Cancer Centers or Veterans' Affairs institutions (all cancers). Conclusions:Wait times for cancer treatment have increased over the last decade. As case loads increase, wait times for treatment are likely to continue increasing, potentially resulting in additional treatment delay. Additional resources and strategies are needed to reduce wait times for cancer treatment in the United States.
The Comparative Reliability and Feasibility of the Past-Year Canadian Diet History Questionnaire II: Comparison of the Paper and Web Versions

Advances in technology-enabled dietary assessment include the advent of web-based food frequency questionnaires, which may reduce costs and researcher burden but may introduce new challenges related to internet connectivity and computer literacy. The purpose of this study was to evaluate the intra- and inter-version reliability, feasibility and acceptability of the paper and web Canadian Diet History Questionnaire II (CDHQ-II) in a sub-sample of 648 adults (aged 39–81 years) recruited from Alberta’s Tomorrow Project. Participants were randomly assigned to one of two groups: (1) paper, web, paper; or (2) web, paper, web over a six-week period. With few exceptions, no statistically significant differences in mean nutrient intake were found in the intra- and inter-version reliability analyses. The majority of participants indicated future willingness to complete the CDHQ-II online, and 59% indicated a preference for the web over the paper version. Findings indicate that, in this population of adults drawn from an existing cohort, the CDHQ-II may be administered in paper or web modalities (increasing flexibility for questionnaire delivery), and the nutrient estimates obtained with either version are comparable. We recommend that other studies explore the feasibility and reliability of different modes of administration of dietary assessment instruments prior to widespread implementation.
Find their Level

Dans beaucoup de « pays en voie de developpement » et dans les nations africaines sortant d'un conflit arme, on a vante les merites du tourisme culturel comme une source essentielle de revenu pour faire redemarrer le developpement national. Cette tendance a entraine une ruee chez les fonctionnaires africains pour vendre une certaine image de leur pays dans le but d'attirer la clientele « de la diaspora » : les descendants du Middle Passage qui voyagent en Afrique a la recherche de « leurs racines » culturelles et historiques. Cette nouvelle situation est encore compliquee par le fait que l'organisation et la realisation d'un programme de promotion nationale negligent frequemment le citoyen ordinaire. Ainsi, le programme de ces Etats-nations est parfois en desaccord avec les aspirations des habitants locaux et des touristes pan-africains. De plus, cette tendance a contribue a un derapage conceptuel considerable, et a eu, pour consequence, des debats vehements sur le sens et sur les criteres de l'africanite. Dans d'autres cas, cette situation a transforme et durci les idees recues sur l'identite africaine. Une comparaison ethnographique d'un pays en developpement, le Ghana, avec un pays sortant d'un conflit arme, le Sierra Leone, peut approfondir et diversifier la comprehension de ce phenomene panafricain emergent ainsi que de ses possibilites afferentes comme de ses limites. Nous examinons comment ces interets complementaires et contradictoires, ces croyances et ces pratiques convergent pour former de nouveaux modes de pelerinage, de nationalite, de dialogue transnational et de mondialisation.
A Readiness Model for Software Development Outsourcing Vendors

Software development outsourcing has been growing steadily. However significant outsourcing failure rates have also been reported. One of the major issues in outsourcing business is that many organisations undertake software outsourcing initiatives without knowing whether or not they are ready to undertake them. The objective of this project is to develop a readiness model in order to measure the organisationpsilas (vendor) readiness for software development outsourcing. Two types of data will be collected in this research project: firstly, factors that can have a positive or negative impact on software outsourcing clients in the selection of software development outsourcing vendors; and secondly, how one can implement these factors. The anticipated outcome of this project will be a software outsourcing readiness model to assist software practitioners in the design of effective software outsourcing strategies. This model should assist outsourcing vendors in measuring the strength or weakness of software outsourcing activities.
Academic Motivation and School Performance: Toward a Structural Model

Abstract The purpose of this study was to propose and test a motivational model of school performance based on Deci and Ryan′s theoretical framework (Deci & Ryan, 1985, 1991) using structural equation modeling. Students completed the French version of the Academic Motivation Scale as well as measures of perceived academic competence and perceived academic self-determination during the spring semester. Subsequently, their final grades in four central subjects were collected at the end of the school year. Results supported the hypothesized model. More specifically, perceived academic competence and perceived academic self-determination positively influenced autonomous academic motivation, which in turn had a positive impact on school performance. The proposed model explained 28% of the variance in performance. Results highlight the importance of academic motivation in the prediction of school performance and future research directions are offered.
Validation of Scores/Measures from a K-2 Developmental Assessment in Mathematics

This study describes psychometric investigations of a developmental assessment in mathematics composed of 19 performance tasks. Techniques from classical and the many-faceted Rasch approaches were combined to analyze field test data from a mixedage sample (n = 110). Descriptive statistics on scores from the overall scale and subdomains indicated increased proficiency with age. Convergent validity coefficients of scores with scaled scores of the Stanford Achievement Test mathematics battery ranged from . 22 to . 57; internal consistency reliability of the total scores on proficiency and independence were . 90 and . 92, respectively; and median interrater reliability was . 80. Classical item statistics and Rasch logit difficulties of tasks suggested an ordered scale structure, although eight tasks did not fit Rasch criteria. The original and calibrated task orderings were consistent at the extreme ends of the scale. Findings point to directions for future improvement of the scale and rater training programs.
The clinical spectrum of amiodarone-associated optic neuropathy.

PURPOSE To describe the clinical spectrum of amiodarone-associated optic neuropathy. METHODS Observational cases series and review. RESULTS Of 55 cases, the median interval for onset of optic neuropathy was four months after initiating amiodarone; 88% occurred within 12 months. Seven (13%) patients were asymptomatic. Twenty-two (40%) patients presented with sudden visual loss, while 26 (47%) had insidious loss of vision. Visual acuity ranged from 20/15 to light perception; 10 (18%) patients had legal blindness with visual acuity of 20/200 or worse. Visual field loss was present in 91% of cases. Color vision loss was present in eight (40%) of 20 cases. Optic disc edema was present in 85% of cases, while eight (15%) patients had retrobulbar optic neuropathy, without evidence of disc edema. Optic disc edema resolved over a median time of three months. Five patients had raised intracranial pressure on lumbar puncture. CONCLUSION We were able to classify amiodarone-associated optic neuropathy into five clinical categories with respect to temporal characteristics and optic nerve appearance: insidious-onset (43%), acute-onset (28%), retrobulbar (13%), increased intracranial pressure (8%), and delayed-progressive onset (8%). Most cases of optic neuropathy commenced within 12 months of initiating amiodarone, with the median onset being four months. Over 10% of patients will have no visual symptoms at the onset. Ophthalmologic examinations within the first 12 months--and particularly within four months of initiating amiodarone--should improve early detection of amiodarone-associated optic neuropathy.
A Comparison of Middle Class English-Canadian and Italian Mothers’ Beliefs about Children’s Peer-directed Aggression and Social Withdrawal

Middle class mothers of 7-year-olds in Canada and Italy were presented hypothetical scenarios depicting children being aggressive or socially withdrawn. The mothers were asked to indicate how they thought the behaviour was caused, how they would feel if their child displayed it, and what socialisation strategies they would use in reacting to it. Most mothers in both countries indicated that they would resort to moderate to high levels of power assertion in response to children’s aggressive behaviour and responses of low to moderate power in cases of children’s social withdrawal. The Canadian mothers indicated that they would experience generally stronger emotional responses with regard to both types of problematic social behaviour in children. Italian mothers indicated that they would use lower levels of power in response to social withdrawal of girls than boys. These results are considered in the light of known differences in value placed on individual initiative between the two countries, and national differences in gender role expectations.
Family Size in the Peloponnese (Southern Greece) in 1700

This article initially presents a reworking of data in a Venetian census of 1700 for the Peloponnese, a region in southern Greece. The analysis is then compared with one based on another Venetian document dated either to 1702 or 1711, and a mean family size of about 4.0 is confirmed. The calculations for 1700 are refined to produce calculations of mean family size for urban and rural communities (3.60 and 4.17, respectively). The results are then discussed in terms of data from the early nineteenth century for the same region. Conclusions are drawn that support the case for a small mean family size in southern Europe in the eighteenth century and question the continued use of multipliers as high as 5.0 in converting Ottoman fiscal data into population numbers.
A graphical device to represent the outcomes of a logistic regression analysis

Ongoing research on the best way to diagnose prostate cancer has yielded and will continue to yield vast amounts of information. Based on, for example, information from prostate cancer screening trials models have been made that enable urologists to predict which man has prostate cancer on the basis of pre‐biopsy data. In patients with screen detected prostate cancer, the presence of indolent disease can now be identified with reasonable certainty by a different model. For these men active surveillance may be a better option than aggressive treatment with its possible side effects as impotence, incontinence and bowel damage. Both models mentioned above are logistic regression models. Nomograms enable their use in daily clinical practice.