2012 · Nature Methods
Research discovery
Research papers
Search indexed scholarly records by title, author, abstract, DOI, journal, year, citation activity and full-text availability.
1,332 papers found.
2012 · Gender and Behaviour
Senior High School Female Students’ Interest in Physics as a Course of Study at the University Level in Ghana
The study of females‘ interest in physics is an issue of international concern. Of the sciences, physics is the subject in which the increase in the number of females involved has been particularly low. The term 'interest' may usually refers to preference to engage in some types of activities rather than others. This study investigated whether Ghanaian Senior High School female science students would prefer to study physics at the university or not and the reasons for their choice. Two hundred and one final year female students in four Senior High Schools offering biology, chemistry and physics in the Cape Coast Metropolis of the Central Region of Ghana, participated in the study. Data was obtained with Questionnaire on Female Participation in Physics and Interview Protocol, administered to the female students. The findings from the study suggest that female students do not prefer physics as a course of study at the university level due to limited career opportunities in the subject. An implication from this study is that female enrolment in physics will not improve unless information about career awareness in the subject is made available to students. Serious efforts must be made by physics educators as well as Physics Departments to create awareness of career opportunities in the study of physics.
2012 · PubMed
Entry to nursing practice preceptor education and support: could we do it better?
High quality preceptorship during their first year of practice is seen as critical for new graduate nurses' development of competence and confidence. Quality preceptorship is dependent upon skilled and knowledgeable preceptors who are committed to this role. A recent longitudinal evaluation of 21 Nursing Entry to Practice (NETP) programmes in New Zealand identified that preceptorship selection, education and support do not always receive the attention they warrant. Failure to plan preceptor selection leads to ad hoc selection and consequent allocations of many preceptors who may not have attended appropriate education, or have a desire to undertake this role. Such a situation is detrimental to the job satisfaction of both preceptors and new graduate nurses. High workloads, rostering difficulties and increased acuity in many clinical areas often prevent preceptors from attending appropriate education and that, in turn, impacts negatively on the preceptor's expectations and clarity with respect to the role. To offset this effect the authors recommend development of a clearly defined preceptor selection process, along with flexible preceptor education programmes that provide a good foundation for support of new graduates in their first year of practice; but do not increase preceptor workloads.
2012 · Systematic Biology
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
DOI: 10.1093/sysbio/sys0292012 · International Journal of Physics & Chemistry Educ…
Impact of Audio-Visual Aids on Senior High School Students’ Achievement in Physics
This study was aimed at finding out the impact audio-visual-aided instruction on students’ achievement in physics at Cape Coast township of Cape Coast Metropolis, Ghana. The study was a non-randomized pre-test/post-test group design. A total of 65 students in Senior High School (SHS) formed the sample for the study. The students were fourth year science students from two purposefully selected co-educational SHS. The two selected schools were randomly designated experimental and control groups respectively. A validated physics achievement test instrument of a reliability coefficient of 0.76 was administered. Analysis of Covariance (ANCOVA) and t-test statistics were used to test the two hypotheses formulated to guide the study at a significance level 0.05. The results showed that SHS students taught with audio-visual aided instruction performed better than those taught with traditional method. The mean achievement scores of both male and female students improved significantly by the use of the audio-visual aided instruction. It was therefore recommended that SHS physics teachers should explore the use of audio-visual-aided instruction to teach the subject, physics.
DOI: 10.51724/ijpce.v4i1.922012 · AORN Journal
Essentials of Nursing Research: Appraising Evidence for Nursing Practice
Essentials of Nursing Research: Appraising Evidence for Nursing Practice Denise F. Polit, Cheryl Tatano Beck 7th edition 2011, Lippincott Williams & Wilkins 624 pages, paperback
DOI: 10.1016/j.aorn.2011.10.0092012 · BMC Public Health
Health literacy and public health: A systematic review and integration of definitions and models
BACKGROUND: Health literacy concerns the knowledge and competences of persons to meet the complex demands of health in modern society. Although its importance is increasingly recognised, there is no consensus about the definition of health literacy or about its conceptual dimensions, which limits the possibilities for measurement and comparison. The aim of the study is to review definitions and models on health literacy to develop an integrated definition and conceptual model capturing the most comprehensive evidence-based dimensions of health literacy. METHODS: A systematic literature review was performed to identify definitions and conceptual frameworks of health literacy. A content analysis of the definitions and conceptual frameworks was carried out to identify the central dimensions of health literacy and develop an integrated model. RESULTS: The review resulted in 17 definitions of health literacy and 12 conceptual models. Based on the content analysis, an integrative conceptual model was developed containing 12 dimensions referring to the knowledge, motivation and competencies of accessing, understanding, appraising and applying health-related information within the healthcare, disease prevention and health promotion setting, respectively. CONCLUSIONS: Based upon this review, a model is proposed integrating medical and public health views of health literacy. The model can serve as a basis for developing health literacy enhancing interventions and provide a conceptual basis for the development and validation of measurement tools, capturing the different dimensions of health literacy within the healthcare, disease prevention and health promotion settings.
DOI: 10.1186/1471-2458-12-802012 · PLoS ONE
Pre-Vaccination Nasopharyngeal Pneumococcal Carriage in a Nigerian Population: Epidemiology and Population Biology
BACKGROUND: Introduction of pneumococcal vaccines in Nigeria is a priority as part of the Accelerated Vaccine Introduction Initiative (AVI) of the Global Alliance for Vaccines and Immunisation (GAVI). However, country data on the burden of pneumococcal disease (IPD) is limited and coverage by available conjugate vaccines is unknown. This study was carried out to describe the pre vaccination epidemiology and population biology of pneumococcal carriage in Nigeria. METHODS: This was a cross sectional survey. Nasopharyngeal swabs (NPS) were obtained from a population sample in 14 contiguous peri-urban Nigerian communities. Data on demographic characteristics and risk factor for carriage were obtained from all study participants. Pneumococci isolated from NPS were characterised by serotyping, antimicrobial susceptibility and Multi Locus Sequencing Typing (MLST). RESULTS: The prevalence of pneumococcal carriage was 52.5%. Carriage was higher in children compared to adults (67.4% vs. 26%), highest (≈90%) in infants aged <9 months and reduced significantly with increasing age (P<0.001). Serotypes 19F (18.6%) and 6A (14.4%) were most predominant. Potential vaccine coverage was 43.8%, 45.0% and 62% for PCV-7, PCV-10 and PCV-13 respectively. There were 16 novel alleles, 72 different sequence types (STs) from the isolates and 3 Sequence Types (280, 310 and 5543) were associated with isolates of more than one serotype indicative of serotype switching. Antimicrobial resistance was high for cotrimoxazole (93%) and tetracycline (84%), a third of isolates had intermediate resistance to penicillin. Young age was the only risk factor significantly associated with carriage. CONCLUSIONS: Pneumococcal carriage and serotype diversity is highly prevalent in Nigeria especially in infants. Based on the coverage of serotypes in this study, PCV-13 is the obvious choice to reduce disease burden and prevalence of drug resistant pneumococci. However, its use will require careful monitoring. Our findings provide sound baseline data for impact assessment following vaccine introduction in Nigeria.
DOI: 10.1371/journal.pone.00305482012 · Open Repository and Bibliography (University of L…
Scikit-learn: Machine Learning in Python
Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.org.
DOI: 10.48550/arxiv.1201.04902012 · IOSR Journal of Applied Chemistry
Langmuir, Freundlich, Temkin and Dubinin–Radushkevich Isotherms Studies of Equilibrium Sorption of Zn 2+ Unto Phosphoric Acid Modified Rice Husk
Equlibrium sorption of the phosphoric acid modified rice husk was studied. The Physico-chemical properties of the modified rice husk were determined. The equilibrium sorption data were fitted into Langmuir, Freundlich, Temkin and Dubinin-Radushkevich (DRK) isotherms. Of the four adsorption isotherm, the R 2 value of Langmuir isotherm model was the highest. The maximum monolayer coverage (Q o ) from Langmuir isotherm model was determined to be 101.01mg/g, the separation factor indicating a favourable sorption experiment is 0.133. Also from Freundlich Isotherm model, the sorption intensity (n) which indicates favourable sorption and the correlation value are 1.6 and 0,89 respectively. The heat of sorption process was estimated from Temkin Isotherm model to be 25.34J/mol and the mean free energy was estimated from DRK isotherm model to be 0.7KJ/mol which vividly proved that the adsorption experiment followed a physical process.
DOI: 10.9790/5736-03138452012 · International review of cytology
Cell Biology of Ischemia/Reperfusion Injury
DOI: 10.1016/b978-0-12-394309-5.00006-72012 · International Journal of Geophysics
Regional Climate Model Sensitivity to Domain Size for the Simulation of the West African Summer Monsoon Rainfall
We use the International Centre for Theoretical Physics (ICTP) Regional Climate Model (RegCM3) to study the impact of different domain sizes on the simulation of the West African summer monsoon rainfall and circulation features. RegCM3 simulates drier conditions over the default domain (RegCM-D1) and its westward extension (RegCM-D2), much less dryness over the eastward extended domain (RegCM-D3) and excessive wetness in the domain extended northward into the extratropical regions (RegCM-D4). This overestimation is related to the existence of larger source of humidity due to the inclusion of a more significant portion of the Atlantic Ocean and to a weakening of the African Easterly Jet (AEJ), which both favor stronger westerlies advecting moisture towards the land. The best performance is, however, captured in the RegCM-D3 experiment, and this originates from a simulation of moderate westerly moisture fluxes along with a stronger AEJ and occurrences of more frequent African Easterly Waves (AEWs). Therefore, the choice of the domain for regional climate model simulation of the West African summer monsoon rainfall is of critical importance, and caution needs to be taken to account for the main regional forcings including mostly the necessary humidity sources of the tropical Atlantic Ocean and the AEWs genesis region upstream of Sudanese Highlands.
DOI: 10.1155/2012/6258312012 · Annals of African Medicine
Biology of breast cancer in Nigerian women: A pilot study
BACKGROUND: Compared to the developed world, there are relatively few studies that describe the tumor biology of breast cancer in African women. While little is known about the tumor biology, clinical and epidemiologic studies suggest that breast cancer in African women are characterized by presentation at late stage and poor clinical outcomes. Analysis of the biological features of breast cancers in Nigerian women was designed to bring additional insight to better understand the spectrum of disease, the phenotypes that present, and the types of interventions that might improve outcomes. MATERIALS AND METHODS: We performed histological analyses for hormone receptors (estrogen and progesterone receptors), HER2, and tumor infiltrating macrophages (TAM) on 17 breast cancers, obtained from Abia State University Teaching Hospital (Aba, Nigeria), between November 2008 and October 2009. On a subset of these cases, we investigated the potential role of a virus in the etiology of these aggressive cancers. RESULTS: The majority of cases in this cohort were characterized as high grade (100% were grade III), triple-negative (65%), and occur in young women (mean age 47 years). We observed high infiltration of TAMs in these tumors, but no evidence of a viral etiology. CONCLUSION: Our findings indicate that breast cancers in Nigerian women have a highly aggressive phenotype (high grade, hormone receptor negative), which is similar to other studies from Africa and other developing nations, as well as from African American women, but is significantly different from Caucasian women in the developed world. The presence of high numbers of TAMs in these tumors raises the possibility of targeting the immune microenvironment for therapeutic interventions.
DOI: 10.4103/1596-3519.968802011 · Methods in Ecology and Evolution
phytools: an R package for phylogenetic comparative biology (and other things)
Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web‐log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
DOI: 10.1111/j.2041-210x.2011.00169.x2011 · BMC Systems Biology
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
BACKGROUND: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. RESULTS: In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. CONCLUSIONS: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.
DOI: 10.1186/1752-0509-5-1982011 · Nature
The Medicago genome provides insight into the evolution of rhizobial symbioses
Sequencing of Medicago truncatula, a model organism of legume biology, shows that genome duplications had a role in the evolution of endosymbiotic nitrogen fixation. Legumes are unusual among plants in that they can carry out endosymbiotic nitrogen fixation with rhizobial bacteria. The genome of Medicago truncatula (also known as barrel medic or barrel clover), a well-established model for the study of legume biology, has now been sequenced. Genome analysis shows that M. truncatula has undergone several rounds of whole-genome duplication, and that the duplication that took place approximately 58 million years ago played an important part in the evolution of endosymbiotic nitrogen fixation. Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.
DOI: 10.1038/nature106252011 · ISRN Ecology
Heavy Metals in Contaminated Soils: A Review of Sources, Chemistry, Risks and Best Available Strategies for Remediation
Scattered literature is harnessed to critically review the possible sources, chemistry, potential biohazards and best available remedial strategies for a number of heavy metals (lead, chromium, arsenic, zinc, cadmium, copper, mercury and nickel) commonly found in contaminated soils. The principles, advantages and disadvantages of immobilization, soil washing and phytoremediation techniques which are frequently listed among the best demonstrated available technologies for cleaning up heavy metal contaminated sites are presented. Remediation of heavy metal contaminated soils is necessary to reduce the associated risks, make the land resource available for agricultural production, enhance food security and scale down land tenure problems arising from changes in the land use pattern.
DOI: 10.5402/2011/4026472011 · Plasmid
Diversity, biology and evolution of IncQ-family plasmids
DOI: 10.1016/j.plasmid.2011.10.0012011 · BMJ
The Cochrane Collaboration's tool for assessing risk of bias in randomised trials
Flaws in the design, conduct, analysis, and reporting of randomised trials can cause the effect of an intervention to be underestimated or overestimated. The Cochrane Collaboration’s tool for assessing risk of bias aims to make the process clearer and more accurate
DOI: 10.1136/bmj.d59282011 · The Lancet
Child and adolescent mental health worldwide: evidence for action
DOI: 10.1016/s0140-6736(11)60827-12011 · Cancer Discovery
The Emergence of lncRNAs in Cancer Biology
Abstract The discovery of numerous noncoding RNA (ncRNA) transcripts in species from yeast to mammals has dramatically altered our understanding of cell biology, especially the biology of diseases such as cancer. In humans, the identification of abundant long ncRNA (lncRNA) &gt;200 bp has catalyzed their characterization as critical components of cancer biology. Recently, roles for lncRNAs as drivers of tumor suppressive and oncogenic functions have appeared in prevalent cancer types, such as breast and prostate cancer. In this review, we highlight the emerging impact of ncRNAs in cancer research, with a particular focus on the mechanisms and functions of lncRNAs. Significance: lncRNAs represent the leading edge of cancer research. Their identity, function, and dysregulation in cancer are only beginning to be understood, and recent data suggest that they may serve as master drivers of carcinogenesis. Increased research on these RNAs will lead to a greater understanding of cancer cell function and may lead to novel clinical applications in oncology. Cancer Discovery; 1(5): 391–407. ©2011 AACR.
DOI: 10.1158/2159-8290.cd-11-02092011 · Nature
Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk
DOI: 10.1038/nature104052011 · Diversity and Distributions
Reproductive biology of Australian acacias: important mediator of invasiveness?
Abstract Aim Reproductive traits are important mediators of establishment and spread of introduced species, both directly and through interactions with other life‐history traits and extrinsic factors. We identify features of the reproductive biology of Australian acacias associated with invasiveness. Location Global. Methods We reviewed the pollination biology, seed biology and alternative modes of reproduction of Australian acacias using primary literature, online searches and unpublished data. We used comparative analyses incorporating an Acacia phylogeny to test for associations between invasiveness and eight reproductive traits in a group of introduced and invasive (23) and non‐invasive (129) species. We also explore the distribution of groups of trait ‘syndromes’ between invasive and non‐invasive species. Results Reproductive trait data were only available for 126 of 152 introduced species in our data set, representing 23/23 invasive and 103/129 non‐invasive species. These data suggest that invasives reach reproductive maturity earlier (10/13 within 2 years vs. 7/26 for non‐invasives) and are more commonly able to resprout (11/21 vs. 13/54), although only time to reproductive maturity was significant when phylogenetic relationships were controlled for. Our qualitative survey of the literature suggests that invasive species in general tend to have generalist pollination systems, prolific seed production, efficient seed dispersal and the accumulation of large and persistent seed banks that often have fire‐, heat‐ or disturbance‐triggered germination cues. Conclusions Invasive species respond quicker to disturbance than non‐invasive taxa. Traits found to be significant in our study require more in‐depth analysis involving data for a broader array of species given how little is known of the reproductive biology of so many taxa in this species‐rich genus. Sets of reproductive traits characteristic of invasive species and a general ability to reproduce effectively in new locations are widespread in Australian acacias. Unless there is substantial evidence to the contrary, care should be taken with all introductions.
DOI: 10.1111/j.1472-4642.2011.00808.x2011 · Modern Applied Science
Floral Biology and Pollination Ecology of Cowpea (Vigna Unguiculata L. Walp)
Studies on the floral biology and pollination ecology of three varieties of cowpea (Vigna unguiculata L. Walp) were carried out. The varieties studied were Var. Oloyin, Var. Sokoto, and Var. Drum. Cowpea is a self pollinated crop which is encouraged by the arrangements of the floral parts. However, Insects visiting cowpea flowers have been implicated in the movement of pollen from one cowpea plant to another. Flower opening of cowpea begins between 6:00am and 6:30am and closes between 11:30am and 12:00pm. Pollen analysis showed similarities in the pollen morphology of the cowpea varieties. Moreover Var. Drum produced the highest number of pollen grains per flower in terms of pollen productivity.
DOI: 10.5539/mas.v5n4p74