Miracle-dz/UniFAR-FTUs huggingface dataset:
Random mutagenesis of yeast 25S rRNA identify bases critical for 60S subunit structural integrity and function

In yeast Saccharomyces cerevisiae, 25S rRNA makes up the major mass and shape of the 60S ribosomal subunit. During translation initiation, the 60S subunit joins the 40S initiation complex, producing the 80S initiation complex. During elongation, the 60S subunit binds the CCA-ends of aminoacyl- and peptidyl-tRNAs at the A-loop and P-loop, respectively, transferring the peptide onto the α-amino group of the aminoacyl-tRNA. To study the role of 25S rRNA in translation in vivo, we randomly mutated 25S rRNA and isolated and characterized seven point mutations that affected yeast cell growth and polysome profiles. Four of these mutations, G651A, A1435U, A1446G and A1587G, change a base involved in base triples crucial for structural integrity. Three other mutations change bases near the ribosomal surface: C2879U and U2408C alter the A-loop and P-loop, respectively, and G1735A maps near a Eukarya-specific bridge to the 40S subunit. By polysome profiling in mmslΔ mutants defective in nonfunctional 25S rRNA decay, we show that some of these mutations are defective in both the initiation and elongation phases of translation. Of the mutants characterized, C2879U displays the strongest defect in translation initiation. The ribosome transit-time assay directly shows that this mutation is also defective in peptide elongation/termination. Thus, our genetic analysis not only identifies bases critical for structural integrity of the 60S subunit, but also suggests a role for bases near the peptidyl transferase center in translation initiation.
Barcoding Sponges: An Overview Based on Comprehensive Sampling

Background Phylum Porifera includes ∼8,500 valid species distributed world-wide in aquatic ecosystems ranging from ephemeral fresh-water bodies to coastal environments and the deep-sea. The taxonomy and systematics of sponges is complicated, and morphological identification can be both time consuming and erroneous due to phenotypic convergence and secondary losses, etc. DNA barcoding can provide sponge biologists with a simple and rapid method for the identification of samples of unknown taxonomic membership. The Sponge Barcoding Project (www.spongebarcoding.org), the first initiative to barcode a non-bilaterian metazoan phylum, aims to provide a comprehensive DNA barcode database for Phylum Porifera. Methodology/Principal Findings ∼7,400 sponge specimens have been extracted, and amplification of the standard COI barcoding fragment has been attempted for approximately 3,300 museum samples with ∼25% mean amplification success. Based on this comprehensive sampling, we present the first report on the workflow and progress of the sponge barcoding project, and discuss some common pitfalls inherent to the barcoding of sponges. Conclusion A DNA-barcoding workflow capable of processing potentially large sponge collections has been developed and is routinely used for the Sponge Barcoding Project with success. Sponge specific problems such as the frequent co-amplification of non-target organisms have been detected and potential solutions are currently under development. The initial success of this innovative project have already demonstrated considerable refinement of sponge systematics, evaluating morphometric character importance, geographic phenotypic variability, and the utility of the standard barcoding fragment for Porifera (despite its conserved evolution within this basal metazoan phylum).
The Quality of Mathematics Instruction in Kindergarten: Associations with Students’ Achievement and Motivation

We examined associations between the quality of kindergarten teachers’ mathematics instruction and their students’ achievement and motivation in mathematics. Using a sample of 20 kindergarten teachers and their 285 students, we rated 5 video-recorded mathematics lessons per teacher throughout the spring semester with the Mathematical Quality of Instruction (MQI). We collected information about students’ achievement from teacher ratings of student performance relative to state standards and an individually administered standardized measure of mathematical reasoning. We obtained data about students’ mathematics motivation (self-competence beliefs, interest, effort expenditure, and need for support) through individual interviews with the children and via teacher ratings. Multilevel modeling analyses indicated that scores on the MQI’s “ambitious mathematics instruction” scale and the “whole lesson” scale predicted students’ end-of-year progress on kindergarten mathematics standards but not their standardized test scores. The whole lesson scores were associated with teacher-rated students’ motivation for mathematics (interest and need for support).
Spatial Correlation Function and Pairwise Velocity Dispersion of Galaxies: Cold Dark Matter Models versus the Las Campanas Survey

We show, with the help of large N-body simulations, that both the real-space two-point correlation function and pairwise velocity dispersion of galaxies can be measured reliably from the Las Campanas Redshift Survey. The real-space correlation function is well fitted by the power law ξ(r) = (r0/r)γ with r0 = (5.06 ± 0.12) h-1 Mpc and γ = 1.862 ± 0.034, and the pairwise velocity dispersion at 1 h-1 Mpc is 570 ± 80 km s-1. A detailed comparison between these observational results and the predictions of current cold dark matter (CDM) cosmogonies is carried out. We construct 60 mock samples for each theoretical model from a large set of high-resolution N-body simulations, which allows us to include various observational selection effects in the analyses and to use exactly the same methods for both real and theoretical samples. We demonstrate that such a procedure is essential in the comparison between models and observations. The observed two-point correlation function is significantly flatter than the mass correlation function in current CDM models on scales ≲1 h-1 Mpc. The observed pairwise velocity dispersion is also lower than that of dark matter particles in these models. We propose a simple antibias model to explain these discrepancies. This model assumes that the number of galaxies per unit dark matter mass, N/M, decreases with the mass of dark haloes. The predictions of CDM models with σ8 Ω0. 60~0.4-0.5 and Γ ~ 0.2 are in agreement with the observational results, if the trend of N/M with M is at the level already observed for rich clusters of galaxies. Thus CDM models with Γ ~ 0.2 and with cluster-abundance normalization are consistent with the observed correlation function and pairwise velocity dispersion of galaxies. A high level of velocity bias is not required in these models.
Disability associated with psychiatric comorbidity and health status in Bosnian refugees living in Croatia.

CONTEXT The relationship between psychiatric symptoms and disability in refugee survivors of mass violence is not known. OBJECTIVE To determine if risk factors, such as demographics, trauma, health status, and psychiatric illness, are associated with disability in Bosnian refugees. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional survey conducted in 1996 of Bosnian refugee adults living in a camp established by the Croatian government near the city of Varazdin. One adult aged 18 years or older was randomly selected from each of 573 camp families; 534 (93%) agreed to participate (mean age, 50 years; 41% male). MAIN OUTCOME MEASURES Culturally validated measures for depression and posttraumatic stress disorder (PTSD) included the Hopkins Symptom Checklist 25 and the Harvard Trauma Questionnaire, respectively. Disability measures included the Medical Outcomes Study Short-Form 20, a physical functioning scale based on World Health Organization criteria, and self-reports of socioeconomic activity, levels of physical energy, and perceived health status. RESULTS Respondents reported a mean (SD) of 6.5 (4.7) unduplicated trauma events; 18% (n=95) had experienced 1 or more torture events. While 55.2% reported no psychiatric symptoms, 39.2% and 26.3% reported symptoms that meet DSM-IV criteria for depression and PTSD, respectively; 20.6% reported symptoms comorbid for both disorders. A total of 25.5% reported having a disability. Refugees who reported symptoms comorbid for both depression and PTSD were associated with an increased risk for disability compared with asymptomatic refugees (unadjusted odds ratio [OR], 5.02; 95% confidence interval [CI], 3.05-8.26; adjusted OR, 2.06; 95% CI, 1.10-3.86). Older age, cumulative trauma, and chronic medical illness were also associated with disability. CONCLUSIONS In a population of Bosnian refugees who had recently fled from the war in Bosnia and Herzegovina, psychiatric comorbidity was associated with disability independent of the effects of age, trauma, and health status.
Mortality experience in relation to a measured arsenic trioxide exposure

This report examines the mortality experience of 527 men who retired from a copper smelter where they were exposed to airborne arsenic trioxide. Urinary arsenic values of all plant employees were determined in 1973, and the relative arsenic exposure in the various departments of the plant were determined. The relationship of airborne arsenic concentrations to urinary arsenic values was studied in a separate experiment, and the feasibility of using urinary arsenic values as a measure of arsenic exposure was established. The mortality experience of the cohort under study showed them to have a mortality 12.2% higher than was found for males of the same area at the same ages and in the same time period. The excess mortality was due chiefly to respiratory cancer. When the deaths were classified by total lifetime arsenic exposure, the respiratory cancer mortality was linearly related to the amount of exposure. The 1973 figures for arsenic exposure underestimated the exposure of the cohort group by a factor of possibly 10. Evidence was obtained which suggests that after removal from arsenic exposure, the risk of lung cancer declines. Certain of the data which are presented suggests there may be a threshold value for airborne arsenic trioxide exposure below which no adverse effects may be expected.
Specific Structural Features of Child-Directed Speech Support Young Children's Word Learning

Young children who hear more child-directed speech (CDS) tend to have larger vocabularies later in childhood (e.g., Ramírez-Esparza, García-Sierra, & Kuhl, 2014; Weisleder & Fernald, 2013), but the specific structural characteristics of CDS underlying this link have previously been underspecified. The present studies sought to elucidate how three structural features of parents’ language input – the use of word repetition, isolated words, and discourse continuity – support children’s language learning. In previous research, I showed that repetition of object labels in successive sentences promotes young children’s encoding of new words (Schwab & Lew-Williams, 2016a). Here, Chapter II examines the extent to which parents’ repetition relates to children’s learning at different time points in development. Next, Chapter III examines how parents’ use of isolated words interacts with repetition in promoting children’s learning of new words. Finally, Chapter IV investigates how continuity of reference promotes children’s learning. Collectively, these studies reveal that the packaging of information within childdirected speech influences children’s word learning, although the extent to which each structure matters depends on children’s level of language knowledge.
Apolipoprotein A-IMilano and 1-Palmitoyl-2-oleoyl Phosphatidylcholine Complex (ETC-216) Protects the in Vivo Rabbit Heart from Regional Ischemia-Reperfusion Injury

Ex vivo studies demonstrated that a synthetic high-density lipoprotein (HDL) comprised of a complex of recombinant apolipoprotein A-IMilano and 1-palmitoyl-2-oleoyl phosphatidylcholine protects the isolated rabbit heart from reperfusion injury. Therefore, we sought to determine whether a pharmaceutical preparation of this complex, ETC-216, was cardioprotective in an in vivo model of left anterior descending artery (LAD) occlusion and reperfusion. Initially, ETC-216 (100 mg/kg) was tested in acute (one-treatment) and chronic (two-treatment) i.v. administrations. ETC-216-treated rabbits developed smaller infarcts expressed as percentage of area at risk (p < 0.01) compared with vehicle treatments. No differences were noted between chronic and acute administration. Therefore, ETC-216 (10, 3, or 1 mg/kg) or equivalent vehicle volumes were acutely infused. Compared with vehicle, ETC-216 reduced infarct size as a percentage of the area at risk at 10 (p < 0.0005) and 3 mg/kg (p < 0.05). No significant differences occurred at 1 mg/kg. To determine whether ETC-216 could protect the heart after initiation of ischemia, the synthetic HDL (10 mg/kg) was infused intravenously beginning 5 min before the end of 30 min of LAD occlusion. Infarct size as percentage of the area at risk was 31.6 ± 3.0 (ETC-216) versus 49.5 ± 2.5 (vehicle) (p < 0.001), and as percentage of left ventricle was 19.7 ± 1.6 (ETC-216) versus 34.1 ± 2.3 (vehicle) (p < 0.0005). Electron microscopy demonstrated that ETC-216 prevented irreversible cardiac damage as assessed by mitochondrial granulation and sarcomere contraction band formation. These findings suggest ETC-216 reduces reperfusion injury and may have utility for coronary artery revascularization procedures.
Teacher Attitudes toward Peer Evaluation: What Shapes Them?.

Teachers from six California school districts were interviewed about their attitudes regarding peer evaluation and the reasons behind those attitudes. Three of the districts were represented by a bargaining agent for the California Federation of Teachers (CFT) and three had California Teachers Association (CTA) representation. Chosen to represent a cross-section, 15 teachers from each district were interviewed; focus was on identifying teachers who might be expected to be active in their teacher unions and who might have influence on the views of their colleagues/peers. For each district and for each question from the semi-structured interview schedule, a mez:m response was computed. A mean for all districts and the standard deviation of those means were then calculated. The district means were tested for significance differences from that composite mean. Results indicate that: teachers would be more open to peer review if the structure of evaluation was changed from the present structure; teachers represented by the CTA tended to be more distrustful of administration; professionalism is a real interest of many teachers, particularly those not nearin= retirement; and opposition to peer review is no longer the monolith of years past. In general, when teachers have no access to peer evaluation, they tend to be opposed to the idea. Interview questions are included. (TJH) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document.
Estimation of cost efficiency with heteroscedasticity: an application to electricity utilities

SUMMARY This paper deals with the estimation of efficiency. Efficiency is measured relative to the cost frontier which is defined as C*(W, 1) = minx{ W'Xf(X) 3 Y X X O} where W is the vector of input prices, X is the vector of inputs, Y is the actual output produced and ft ) is a function of the production technology. The condition J(X) > Y, X 0 implies that the maximum possible output, given X 3 0, can never be less than the actual output. A firm is defined as cost inefficient if its actual cost exceeds the minimum cost given by the cost frontier, which is to be estimated by using data on actual costs, output and input prices. We first consider a panel data model where cost inefficiency is decomposed into a permanent component and a residual component. The model can be viewed as a one-way error component model (ECM) with an additional error term introduced to capture the residual component of cost inefficiency. Second, the ECM is generalized to accommodate firm-specific variances for the permanent inefficiency component. Finally, we propose a multistep procedure to estimate the cost function parameters and to predict cost inefficiency. The model is applied to examine efficiency in the production of electricity by 10 major investor-owned electricity utilities in Texas during 1966-85. The production technology is represented by a cost function that is assumed to be the same for every utility (except for heterogeneous intercepts), but it is allowed to shift over time owing to changes in technology. Empirically we find evidence for permanent and residual cost inefficiencies. Furthermore, the data support the ECM with firm-specific variances and rejects the homoscedastic ECM. Cost inefficiency is found to vary widely across utilities, ranging from 8% to 36% with a mean of 27%. Technical change, defined as the rate of cost diminution over time with everything else unchanged, is found to be quite small (less than ? 1%), especially during 1971-85.
The Design of Assistive Location-based Technologies for People with Ambulatory Disabilities: A Formative Study

In this paper, we investigate how people with mobility impairments assess and evaluate accessibility in the built environment and the role of current and emerging location-based technologies therein. We conducted a three-part formative study with 20 mobility impaired participants: a semi-structured interview (Part 1), a participatory design activity (Part 2), and a design probe activity (Part 3). Part 2 and 3 actively engaged our participants in exploring and designing the future of what we call assistive location-based technologies (ALTs) location-based technologies that specifically incorporate accessibility features to support navigating, searching, and exploring the physical world. Our Part 1 findings highlight how existing mapping tools provide accessibility benefits even though often not explicitly designed for such uses. Findings in Part 2 and 3 help identify and uncover useful features of future ALTs. In particular, we synthesize 10 key features and 6 key data qualities. We conclude with ALT design recommendations.
How did general practitioners protect themselves, their family, and staff during the SARS epidemic in Hong Kong?

Context: Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease and how the frontline community doctors respond to it is not known. Objectives: To explore the impact of SARS on general practitioners (GPs) in Hong Kong. Design: A cross sectional survey. Setting: Community based primary care clinics. Participants: 183 family medicine tutors affiliated with a local university. Postal survey sent to all tutors with a 74.8% response rate. Main outcome measures: Change of clinical behaviour and practices during the epidemic; anxiety level of primary care doctors. Results: All agreed SARS had changed their clinical practices. Significant anxiety was found in family doctors. Three quarters of respondents recalled requesting more investigations while a quarter believed they had over-prescribed antibiotics. GPs who were exposed to SARS or who had worked in high infection districts were less likely to quarantine themselves (10.8% versus 33.3%; p<0.01; 6.5% versus 27.5%; p<0.01 respectively). Exposure to SARS, the infection rates in their working district, and anxiety levels had significant impact on the level of protection or prescribing behaviour. Conclusion: The clinical practice of GPs changed significantly as a result of SARS. Yet, those did not quarantine themselves suggesting other factors may have some part to play. As failure to apply isolation precautions to suspected cases of SARS was one major reason for its spread, a contingency plan from the government to support family doctors is of utmost importance. Interface between private and public sectors are needed in Hong Kong to prepare for any future epidemics.
Conjugate Analysis of the Conway-Maxwell-Poisson Distribution

This article explores a Bayesian analysis of a generalization of the Poisson distribution. By choice of a second parameter , both under-dispersed and over-dispersed data can be modeled. The Conway-Maxwell-Poisson distribu- tion forms an exponential family of distributions, so it has sucien t statistics of xed dimension as the sample size varies, and a conjugate family of prior distribu- tions. The article displays and proves a necessary and sucien t condition on the hyperparameters of the conjugate family for the prior to be proper, and it discusses methods of sampling from the conjugate distribution. An elicitation program to nd the hyperparameters from the predictive distribution is also discussed.
working with diversity : a framework for action

The Consultative Group on International Agricultural Research (CGIAR) Centers have committed to working with diversity in their organizations in an explicit and intentional way. This new diversity initiative builds on earlier work on gender staffing while developing new concepts, approaches, methods, and tools to engage the more complex challenges of working effectively with multiple dimensions of diversity. This report provides the first building block in this effort. It synthesizes research and experience in working with organizational diversity in a way that is meaningful for the context and needs of the Centers. The aim is to provide a solid foundation of knowledge and understanding from which the individual Centers, as well as the CGIAR System as a whole, can craft a unique approach to working with diversity tailored to their specific needs, aspirations, and contexts. The report is structured around three guiding questions: What are the motive forces dribing our need to work more intentionally with diversity? How do we define and understand diversity in a way that is meaningful for this organization? Which change strategies, methods, and tools will be most effective given our objectives and approach to working with diversity?
Paclitaxel-coated expanded polytetrafluoroethylene haemodialysis grafts inhibit neointimal hyperplasia in porcine model of graft stenosis.

BACKGROUND The main pathology of haemodialysis graft stenosis is venous neointimal hyperplasia at graft-venous anastomoses. Neointimal hyperplasia is also observed in cases of coronary artery in-stent restenosis. Paclitaxel is a chemotherapeutic agent used to treat cancer, and has been proven to inhibit neointimal hyperplasia of coronary artery in-stent restenosis. In this study, we examined whether a paclitaxel-coated haemodialysis graft could inhibit neointimal hyperplasia and prevent stenosis. METHODS We dip-coated paclitaxel on expanded polytetrafluoroethylene (ePTFE) grafts at a dose density of 0.59 microg/mm(2). In vitro release tests showed an initial paclitaxel burst followed by a long-term slow release. Using ePTFE grafts with (coated group, n = 8) or without a paclitaxel coating (control group, n = 11), we constructed arteriovenous (AV) grafts connecting the common carotid artery and the external jugular vein in Landrace pigs. RESULTS After excluding seven pigs for technical failure, cross-sections of graft-venous anastomoses obtained 6 weeks after placing the AV grafts were analysed. Percentage luminal stenosis, ratios of intima to media in whole cross-sections, areas of intima in the peri-junctional areas (within 2 mm above and 2 mm below the graft-venous junction), and the mean thickness of intima within venous sides of cross-sections, were 60.5% (range, 41.5-60.7), 13.0 (range, 8.6-20.4), 23.7 mm(2) (range, 10.8-32.1) and 2.1 mm (range, 1.1-3.0), respectively, in the control group, whereas corresponding median values in the coated group were 10.4% (range, 1.0-17.8), 1.0 (range, 0.7-5.1), 1.6 mm(2) (range, 0.2-8.0) and 0.3 mm (range, 0.1-2.2). All parameters were significantly different between the two groups (P<0.05 by Mann-Whitney test). CONCLUSION Paclitaxel-coated ePTFE grafts could prevent neointimal hyperplasia and the stenosis of AV haemodialysis grafts.