0.25 µL: ± 6%; ± 0.015 µL
1.25 µL: ± 1.5%; ± 0.01875 µL
2.5 µL: ± 0.7%; ± 0.0175 µL
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Home » Research Paper – Structure, Examples and Writing Guide
Table of Contents
Definition:
Research Paper is a written document that presents the author’s original research, analysis, and interpretation of a specific topic or issue.
It is typically based on Empirical Evidence, and may involve qualitative or quantitative research methods, or a combination of both. The purpose of a research paper is to contribute new knowledge or insights to a particular field of study, and to demonstrate the author’s understanding of the existing literature and theories related to the topic.
The structure of a research paper typically follows a standard format, consisting of several sections that convey specific information about the research study. The following is a detailed explanation of the structure of a research paper:
The title page contains the title of the paper, the name(s) of the author(s), and the affiliation(s) of the author(s). It also includes the date of submission and possibly, the name of the journal or conference where the paper is to be published.
The abstract is a brief summary of the research paper, typically ranging from 100 to 250 words. It should include the research question, the methods used, the key findings, and the implications of the results. The abstract should be written in a concise and clear manner to allow readers to quickly grasp the essence of the research.
The introduction section of a research paper provides background information about the research problem, the research question, and the research objectives. It also outlines the significance of the research, the research gap that it aims to fill, and the approach taken to address the research question. Finally, the introduction section ends with a clear statement of the research hypothesis or research question.
The literature review section of a research paper provides an overview of the existing literature on the topic of study. It includes a critical analysis and synthesis of the literature, highlighting the key concepts, themes, and debates. The literature review should also demonstrate the research gap and how the current study seeks to address it.
The methods section of a research paper describes the research design, the sample selection, the data collection and analysis procedures, and the statistical methods used to analyze the data. This section should provide sufficient detail for other researchers to replicate the study.
The results section presents the findings of the research, using tables, graphs, and figures to illustrate the data. The findings should be presented in a clear and concise manner, with reference to the research question and hypothesis.
The discussion section of a research paper interprets the findings and discusses their implications for the research question, the literature review, and the field of study. It should also address the limitations of the study and suggest future research directions.
The conclusion section summarizes the main findings of the study, restates the research question and hypothesis, and provides a final reflection on the significance of the research.
The references section provides a list of all the sources cited in the paper, following a specific citation style such as APA, MLA or Chicago.
You can write Research Paper by the following guide:
Note : The below example research paper is for illustrative purposes only and is not an actual research paper. Actual research papers may have different structures, contents, and formats depending on the field of study, research question, data collection and analysis methods, and other factors. Students should always consult with their professors or supervisors for specific guidelines and expectations for their research papers.
Research Paper Example sample for Students:
Title: The Impact of Social Media on Mental Health among Young Adults
Abstract: This study aims to investigate the impact of social media use on the mental health of young adults. A literature review was conducted to examine the existing research on the topic. A survey was then administered to 200 university students to collect data on their social media use, mental health status, and perceived impact of social media on their mental health. The results showed that social media use is positively associated with depression, anxiety, and stress. The study also found that social comparison, cyberbullying, and FOMO (Fear of Missing Out) are significant predictors of mental health problems among young adults.
Introduction: Social media has become an integral part of modern life, particularly among young adults. While social media has many benefits, including increased communication and social connectivity, it has also been associated with negative outcomes, such as addiction, cyberbullying, and mental health problems. This study aims to investigate the impact of social media use on the mental health of young adults.
Literature Review: The literature review highlights the existing research on the impact of social media use on mental health. The review shows that social media use is associated with depression, anxiety, stress, and other mental health problems. The review also identifies the factors that contribute to the negative impact of social media, including social comparison, cyberbullying, and FOMO.
Methods : A survey was administered to 200 university students to collect data on their social media use, mental health status, and perceived impact of social media on their mental health. The survey included questions on social media use, mental health status (measured using the DASS-21), and perceived impact of social media on their mental health. Data were analyzed using descriptive statistics and regression analysis.
Results : The results showed that social media use is positively associated with depression, anxiety, and stress. The study also found that social comparison, cyberbullying, and FOMO are significant predictors of mental health problems among young adults.
Discussion : The study’s findings suggest that social media use has a negative impact on the mental health of young adults. The study highlights the need for interventions that address the factors contributing to the negative impact of social media, such as social comparison, cyberbullying, and FOMO.
Conclusion : In conclusion, social media use has a significant impact on the mental health of young adults. The study’s findings underscore the need for interventions that promote healthy social media use and address the negative outcomes associated with social media use. Future research can explore the effectiveness of interventions aimed at reducing the negative impact of social media on mental health. Additionally, longitudinal studies can investigate the long-term effects of social media use on mental health.
Limitations : The study has some limitations, including the use of self-report measures and a cross-sectional design. The use of self-report measures may result in biased responses, and a cross-sectional design limits the ability to establish causality.
Implications: The study’s findings have implications for mental health professionals, educators, and policymakers. Mental health professionals can use the findings to develop interventions that address the negative impact of social media use on mental health. Educators can incorporate social media literacy into their curriculum to promote healthy social media use among young adults. Policymakers can use the findings to develop policies that protect young adults from the negative outcomes associated with social media use.
References :
Appendix : The survey used in this study is provided below.
Social Media and Mental Health Survey
Thank you for your participation!
Research papers have several applications in various fields, including:
Research papers are typically written when a person has completed a research project or when they have conducted a study and have obtained data or findings that they want to share with the academic or professional community. Research papers are usually written in academic settings, such as universities, but they can also be written in professional settings, such as research organizations, government agencies, or private companies.
Here are some common situations where a person might need to write a research paper:
The purpose of a research paper is to present the results of a study or investigation in a clear, concise, and structured manner. Research papers are written to communicate new knowledge, ideas, or findings to a specific audience, such as researchers, scholars, practitioners, or policymakers. The primary purposes of a research paper are:
Research papers have several characteristics that distinguish them from other forms of academic or professional writing. Here are some common characteristics of research papers:
Research papers have many advantages, both for the individual researcher and for the broader academic and professional community. Here are some advantages of research papers:
Research papers also have some limitations that should be considered when interpreting their findings or implications. Here are some common limitations of research papers:
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We are seeking to recruit a Quantitative Research Assistant who will work as part of the Young Lives research team to support agreed research priorities. The post holder will be expected to work collaboratively with researchers and policy staff in Oxford and the four Young Lives study countries.
The position of Quantitative Research Assistant emphasises analysis of quantitative data and requires strong quantitative analysis skills and interpersonal/team-working skills. The post-holder will be responsible to the Young Lives Quantitative Research Officer.
Key Responsibilities:
The successful candidate will have a Master’s degree completed by October 2024 in a quantitative social science discipline (e.g. economics, social statistics). They will also have proficiency in using the STATA statistical package for data management, manipulation and analysis. High level written communication skills in English are essential for this role.
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by CBS News
Despite growing research that points to the negative health impacts of alcohol, many Americans are unaware of the connection between drinking and cancer risk.
A recent report from the American Association for Cancer Research found excessive levels of alcohol consumption increase the risk for six different types of cancer, including:
"Some of this is happening through chronic inflammation. We also know that alcohol changes the microbiome, so those are the bacteria that live in your gut, and that can also increase the risk," Dr. Céline Gounder, CBS News medical contributor and editor-at-large for public health at KFF Health News, recently said on "CBS Mornings."
But how much is too much when it comes to drinking? We asked experts what to know:
How much alcohol is bad for you?
"Excessive levels of alcohol" equates to about three or more drinks per day for women and four or more drinks per day for men, Gounder said.
According to the National Institute on Alcohol Abuse and Alcoholism, a standard alcoholic drink contains 14 grams (or 0.6 ounces) of pure alcohol. Generally, this amount is found in 12 ounces of beer, 5 ounces of wine and 1.5 ounces, or a "shot," of 80-proof distilled spirits or liquor.
Other studies have shown, however, there is no "safe amount" of alcohol, Gounder said, particularly if you have underlying medical conditions.
"If you don't drink, don't start drinking. If you do drink, really try to keep it within moderation," she said.
Dr. Amy Commander, medical director of the Mass General Cancer Center specializing in breast cancer, told CBS News alcohol is the third leading modifiable risk factor that can increase cancer risk after accounting for cigarette smoking and excess body weight.
"There really isn't a safe amount of alcohol for consumption," she said. "In fact, it's best to not drink alcohol at all, but that is obviously hard for many people. So I think it's really important for individuals to just be mindful of their alcohol consumption and certainly drink less."
How else can alcohol affect your health?
The benefits of limiting alcohol is not just about cancer risk. Alcohol in large or frequent amounts is considered toxic to the human body, said Dr. Angela Tatiana Alistar, medical director of GI Medical Oncology at Morristown Medical Center, Atlantic Health System.
"All organs can be affected by alcohol intake depending on dose and frequency," she told CBS News. "There is vast scientific literature regarding the impact of alcohol consumption on the liver described as hepatitis (in the acute form), liver cirrhosis (chronic form) and possible liver cancer."
Drinking alcohol can also have direct and immediate effects on other organs like the brain, affecting the sleep-wake cycle.
"It can also affect cognition, coordination and emotional regulation," Alistar said. "Acute and chronic dependence and tolerance to alcohol is a high-risk factor for social functioning and mental health."
Is wine healthy?
Some studies have suggested health benefits from drinking red wine . Occasional wine is also a part of the Mediterranean diet, which is often praised for a reduction in mortality, heart disease and more. But, other research says any potential benefit doesn't outweigh the risks.
"A glass of red wine is included in terms of the alcoholic beverages that one should be mindful of — beer, red wine, other spirits," said Commander. "There's been at times this health halo about red wine, but when it comes to cancer, it is still considered alcohol and it should be limited."
But, doesn't everything cause cancer anyway?
Commander admits cancers are complex with many factors that can contribute to someone's risk — but, at the same time, we're making strides in cure rates and early detection.
For example, the latest Cancer Progress Report found a 33% reduction in the overall cancer deaths from 1991 to 2021.
"So that is hopeful," Commander said, adding alcohol is just "one piece of the puzzle" in prevention.
"There are so many aspects of our lifestyle that we should focus on in order to optimize our health, certainly to reduce our risk of cancer, but also other chronic diseases, such as cardiovascular disease, Type 2 diabetes and other conditions that we face in this country," she said.
Alistar recognizes social changes can be difficult when it comes to alcohol.
"Socializing with friends and family typically involves sharing food and drinks. Having open conversations about the impact of alcohol on general health with your family and friends would be a good way to start," she said, but added "celebratory drinks or foods are OK in my opinion if most of the time one has a healthy diet and lifestyle."
Other ways to decrease cancer risk
Reducing alcohol isn't the only way to decrease your risk of cancer. There are several other modifiable risk factors that researchers found are linked to more than 40% of all cancer fatalities, including smoking, excess body weight, physical inactivity and diet.
Using sunscreen to prevent skin cancer and getting the HPV vaccine to prevent cervical cancer and oral cancer related to the human papillomavirus are other prevention measures, Gounder said.
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Methodology
Research methods are specific procedures for collecting and analyzing data. Developing your research methods is an integral part of your research design . When planning your methods, there are two key decisions you will make.
First, decide how you will collect data . Your methods depend on what type of data you need to answer your research question :
Second, decide how you will analyze the data .
Methods for collecting data, examples of data collection methods, methods for analyzing data, examples of data analysis methods, other interesting articles, frequently asked questions about research methods.
Data is the information that you collect for the purposes of answering your research question . The type of data you need depends on the aims of your research.
Your choice of qualitative or quantitative data collection depends on the type of knowledge you want to develop.
For questions about ideas, experiences and meanings, or to study something that can’t be described numerically, collect qualitative data .
If you want to develop a more mechanistic understanding of a topic, or your research involves hypothesis testing , collect quantitative data .
Qualitative | to broader populations. . | |
---|---|---|
Quantitative | . |
You can also take a mixed methods approach , where you use both qualitative and quantitative research methods.
Primary research is any original data that you collect yourself for the purposes of answering your research question (e.g. through surveys , observations and experiments ). Secondary research is data that has already been collected by other researchers (e.g. in a government census or previous scientific studies).
If you are exploring a novel research question, you’ll probably need to collect primary data . But if you want to synthesize existing knowledge, analyze historical trends, or identify patterns on a large scale, secondary data might be a better choice.
Primary | . | methods. |
---|---|---|
Secondary |
In descriptive research , you collect data about your study subject without intervening. The validity of your research will depend on your sampling method .
In experimental research , you systematically intervene in a process and measure the outcome. The validity of your research will depend on your experimental design .
To conduct an experiment, you need to be able to vary your independent variable , precisely measure your dependent variable, and control for confounding variables . If it’s practically and ethically possible, this method is the best choice for answering questions about cause and effect.
Descriptive | . . | |
---|---|---|
Experimental |
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Research method | Primary or secondary? | Qualitative or quantitative? | When to use |
---|---|---|---|
Primary | Quantitative | To test cause-and-effect relationships. | |
Primary | Quantitative | To understand general characteristics of a population. | |
Interview/focus group | Primary | Qualitative | To gain more in-depth understanding of a topic. |
Observation | Primary | Either | To understand how something occurs in its natural setting. |
Secondary | Either | To situate your research in an existing body of work, or to evaluate trends within a research topic. | |
Either | Either | To gain an in-depth understanding of a specific group or context, or when you don’t have the resources for a large study. |
Your data analysis methods will depend on the type of data you collect and how you prepare it for analysis.
Data can often be analyzed both quantitatively and qualitatively. For example, survey responses could be analyzed qualitatively by studying the meanings of responses or quantitatively by studying the frequencies of responses.
Qualitative analysis is used to understand words, ideas, and experiences. You can use it to interpret data that was collected:
Qualitative analysis tends to be quite flexible and relies on the researcher’s judgement, so you have to reflect carefully on your choices and assumptions and be careful to avoid research bias .
Quantitative analysis uses numbers and statistics to understand frequencies, averages and correlations (in descriptive studies) or cause-and-effect relationships (in experiments).
You can use quantitative analysis to interpret data that was collected either:
Because the data is collected and analyzed in a statistically valid way, the results of quantitative analysis can be easily standardized and shared among researchers.
Research method | Qualitative or quantitative? | When to use |
---|---|---|
Quantitative | To analyze data collected in a statistically valid manner (e.g. from experiments, surveys, and observations). | |
Meta-analysis | Quantitative | To statistically analyze the results of a large collection of studies. Can only be applied to studies that collected data in a statistically valid manner. |
Qualitative | To analyze data collected from interviews, , or textual sources. To understand general themes in the data and how they are communicated. | |
Either | To analyze large volumes of textual or visual data collected from surveys, literature reviews, or other sources. Can be quantitative (i.e. frequencies of words) or qualitative (i.e. meanings of words). |
If you want to know more about statistics , methodology , or research bias , make sure to check out some of our other articles with explanations and examples.
Research bias
Quantitative research deals with numbers and statistics, while qualitative research deals with words and meanings.
Quantitative methods allow you to systematically measure variables and test hypotheses . Qualitative methods allow you to explore concepts and experiences in more detail.
In mixed methods research , you use both qualitative and quantitative data collection and analysis methods to answer your research question .
A sample is a subset of individuals from a larger population . Sampling means selecting the group that you will actually collect data from in your research. For example, if you are researching the opinions of students in your university, you could survey a sample of 100 students.
In statistics, sampling allows you to test a hypothesis about the characteristics of a population.
The research methods you use depend on the type of data you need to answer your research question .
Methodology refers to the overarching strategy and rationale of your research project . It involves studying the methods used in your field and the theories or principles behind them, in order to develop an approach that matches your objectives.
Methods are the specific tools and procedures you use to collect and analyze data (for example, experiments, surveys , and statistical tests ).
In shorter scientific papers, where the aim is to report the findings of a specific study, you might simply describe what you did in a methods section .
In a longer or more complex research project, such as a thesis or dissertation , you will probably include a methodology section , where you explain your approach to answering the research questions and cite relevant sources to support your choice of methods.
Other students also liked, writing strong research questions | criteria & examples.
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Introduction, summary of rpfdb features and functionalities, expansion and improvement of the rpfdb database, database usage example, conclusion and discussion, data availability, acknowledgements, rpfdb v3.0: an enhanced repository for ribosome profiling data and related content.
The first two authors should be regarded as Joint First Authors.
Yan Wang, Yuewen Tang, Zhi Xie, Hongwei Wang, RPFdb v3.0: an enhanced repository for ribosome profiling data and related content, Nucleic Acids Research , 2024;, gkae808, https://doi.org/10.1093/nar/gkae808
RPFdb ( http://www.rpfdb.org or http://sysbio.gzzoc.com/rpfdb/ ) is a comprehensive repository dedicated to hosting ribosome profiling (Ribo-seq) data and related content. Herein, we present RPFdb v3.0, a significant update featuring expanded data content and improved functionality. Key enhancements include (i) increased data coverage, now encompassing 5018 Ribo-seq datasets and 2343 matched RNA-seq datasets from 496 studies across 34 species; (ii) implementation of translation efficiency, combining Ribo-seq and RNA-seq data to provide gene-specific translation efficiency; (iii) addition of pausing score, facilitating the identification of condition-specific triplet amino acid motifs with enhanced ribosome enrichment; (iv) refinement of open reading frame (ORF) annotation, leveraging RibORF v2.0 for more sensitive detection of actively translated ORFs; (v) introduction of a resource hub, curating advances in translatome sequencing techniques and data analytics tools to support a panoramic overview of the field; and (vi) redesigned web interface, providing intuitive navigation with dedicated pages for streamlined data retrieval, comparison and visualization. These enhancements make RPFdb a more powerful and user-friendly resource for researchers in the field of translatomics. The database is freely accessible and regularly updated to ensure its continued relevance to the scientific community.
Translation is a highly regulated process that plays a crucial role in shaping cellular proteomes ( 1 ). Its significance extends beyond protein synthesis, serving as a rapid and reversible means of gene regulation that enables cells to respond dynamically to environmental cues and stress conditions ( 2 ). The multi-step nature of translation, including initiation, elongation and termination phases, each regulated by numerous factors, underscores its complexity ( 3 ). Recent years have seen a paradigm shift in our understanding of gene translation and translational regulation. A pivotal advancement in this field is the development of ribosome profiling (Ribo-seq) by Ingolia and Weissman in 2009 ( 4 ). This breakthrough technique revolutionized translatome research, providing an unprecedented, genome-wide, high-resolution view of messenger RNA (mRNA) translation by capturing and sequencing ribosome-protected mRNA fragments.
Since its inception, Ribo-seq has undergone significant methodological refinements to address technical challenges such as ribosome runoff during sample preparation and biases in library construction ( 5 ). These improvements, coupled with advances in bioinformatics ( 6 ), have broadened its applications. Consequently, Ribo-seq has facilitated groundbreaking discoveries: (i) identification of pervasive translation outside annotated protein-coding regions, including within long non-coding RNAs and circular RNAs, challenging traditional definitions of the coding genome ( 7–9 ); (ii) revelation of the prevalence and importance of upstream and downstream open reading frames (ORFs) and alternative start codons in translational control, elucidating novel mechanisms of gene expression regulation ( 10 , 11 ); (iii) insights into phenomena such as ribosome pausing and its role in protein folding and regulation, linking translational kinetics to protein function ( 12 ); (iv) elucidation of translational dysregulation in various pathologies, opening new avenues for therapeutic interventions ( 13 ); and (v) understanding of how viruses hijack and manipulate host translation machinery, informing the development of novel antiviral strategies ( 14 ).
These discoveries have precipitated a surge in Ribo-seq experiments across molecular biology and biomedicine. As researchers increasingly embrace this powerful technique, the growing volume of data has necessitated the creation of dedicated databases for hosting, processing and analyzing this information. These databases range from comprehensive, multi-species repositories such as RPFdb ( 15 ), Trips-Viz ( 16 ), GWIPS-viz ( 17 ) and TranslatomeDB ( 18 ) to more specialized resources such as Ribo-uORF ( 19 ), uORFdb ( 20 ), riboCIRC ( 21 ) and sORFs.org ( 22 ). The development of these databases has significantly reduced technical barriers, democratizing access to this complex data type and enabling researchers without extensive bioinformatics expertise to explore and utilize it effectively.
RPFdb is purpose-built to host Ribo-seq data and related content, processed through a unified pipeline to ensure consistency and comparability across datasets ( 15 , 23 ). To maintain its relevance and utility in this rapidly advancing field, RPFdb now undergoes systematic updates. This iterative process involves not only the addition of new datasets but also the refinement of ORF annotation, incorporation of new analytical contents and enhancement of user interfaces based on user feedback and emerging requirements. By continuously improving and expanding RPFdb, our objective is to provide the ribosome profiling community with a comprehensive, up-to-date resource, facilitating translation of raw sequencing data into meaningful biological insights.
Since its initial release in 2016 ( 23 ), RPFdb has evolved to version 3.0, now offering enhanced capabilities for the exploration of Ribo-seq data and related content. Figure 1 illustrates the key features of RPFdb v3.0, showcasing its comprehensive functionalities for researchers. RPFdb v3.0 maintains its intuitive interface while significantly expanding its functionalities: (i) Browse: enables users to explore an extensive collection of studies and samples with detailed information on data descriptions and data quality assessment; (ii) ORF catalog: presents an updated compilation of actively translated ORFs with enhanced annotation and filtering options; (iii) Quantification: facilitates the visualization of footprints and comparative analysis of RPKM (Reads Per Kilobase per Million mapped reads) values across genomic regions, as well as the assessment of translation efficiency and pausing scores; (iv) Download: provides access to tabular metadata and the latest Ribo-seq and RNA-seq tracks; (v) Statistics: offers graphical summaries of collected data; (vi) Resource: informs users about cutting-edge advances in translatome sequencing techniques and data analytical tools; (vii) Citation: guides proper attribution and usage of the database and (viii) Help: includes a step-by-step tutorial for new users. These enhanced features collectively empower RPFdb to promote collaboration and knowledge sharing within the ribosome profiling community.
Overview of RPFdb features and functionalities.
The evolution of RPFdb into its current version, RPFdb v3.0, represents a significant advancement, particularly in terms of data coverage and diversity (Table 1 ). The database now hosts an extensive collection of 5018 Ribo-seq datasets derived from 496 distinct studies. These datasets encompass a wide spectrum of experimental conditions, tissue types, developmental stages and environmental stimuli, providing researchers with a rich array of biological contexts to explore. A key enhancement in RPFdb v3.0 is the inclusion of 2343 matched RNA-seq datasets. This integration allows for comparative analyses that link translational dynamics with transcriptomic profiles, offering a more comprehensive view of gene expression regulation. The database’s scope has expanded to cover 34 different species, from unicellular microbes to multicellular plants and animals, underscoring its broad applicability across diverse biological systems.
Summary of RPFdb updates
. | Version 1.0 . | Version 2.0 . | Version 3.0 . |
---|---|---|---|
Release date | 2016 | 2019 | 2024 |
Data | |||
Type | Ribo-seq only | Ribo-seq only | Ribo-seq + RNA-seq |
Species | 8 | 29 | 34 |
Studies | 82 | 293 | 496 |
Samples | 777 | 2884 | 5018 + 2343 |
Content | |||
Quality assessment | • Sequencing QC report | • Sequencing QC report | • Sequencing QC report |
• Post-mapping QC report | |||
Expression quantification | • Gene translation (RPKM) | • Gene translation (RPKM, RawCount) | • Gene translation (RPKM, RawCount) |
• Gene transcription (RawCount) | |||
• Translation efficiency | |||
• Pausing score | |||
Translation annotation | • ORF catalog | • ORF catalog | |
• Consensus Ribo-seq ORF set | |||
Coverage track | • Ribo-seq tracks (bigWig) | ||
• RNA-seq tracks (bigWig) |
. | Version 1.0 . | Version 2.0 . | Version 3.0 . |
---|---|---|---|
Release date | 2016 | 2019 | 2024 |
Data | |||
Type | Ribo-seq only | Ribo-seq only | Ribo-seq + RNA-seq |
Species | 8 | 29 | 34 |
Studies | 82 | 293 | 496 |
Samples | 777 | 2884 | 5018 + 2343 |
Content | |||
Quality assessment | • Sequencing QC report | • Sequencing QC report | • Sequencing QC report |
• Post-mapping QC report | |||
Expression quantification | • Gene translation (RPKM) | • Gene translation (RPKM, RawCount) | • Gene translation (RPKM, RawCount) |
• Gene transcription (RawCount) | |||
• Translation efficiency | |||
• Pausing score | |||
Translation annotation | • ORF catalog | • ORF catalog | |
• Consensus Ribo-seq ORF set | |||
Coverage track | • Ribo-seq tracks (bigWig) | ||
• RNA-seq tracks (bigWig) |
The progression from RPFdb v1.0 to v3.0 demonstrates consistent and substantial growth. Each version has markedly increased the number of samples, studies and species represented. Notably, the latest version nearly doubles the Ribo-seq datasets compared with v2.0 and represents more than a 6-fold increase from v1.0. The introduction of matched RNA-seq data further enhances the database’s utility for comprehensive translational studies. This expansion not only increases the quantity of data available but also improves the quality and depth of potential analyses. The broader species coverage facilitates comparative studies across evolutionarily diverse organisms, while the inclusion of matched RNA-seq data enables researchers to distinguish between transcriptional and translational regulation effects.
Actively translated ORFs represent the regions of the genome that are transcribed into mRNA and subsequently translated into proteins. Accurate annotation of actively translated ORFs is crucial for understanding the fundamental mechanisms of gene expression and protein synthesis. We refine actively translated ORF annotations through the use of RibORF v2.0 software ( 24 , 25 ), which automates data quality control, selects 3-nt periodic reads and employs ribosomal A-site corrected reads to identify genome-wide ORFs. To improve the reliability of ORF identification among duplicate samples, we have replaced the previous method of combining Ribo-seq data with duplicate samples. This change allows for a more accurate assessment of ORF consistency across duplicates, providing researchers with more reliable data. In addition to these refined annotations, we offer a consensus set of Ribo-seq ORFs for each species. This consensus set represents a standardized collection by merging RibORF-identified ORFs from different conditions ( 26 ). By providing refined ORF annotations and consensus sets, RPFdb v3.0 not only enhances the accuracy of translational data but also supports more consistent and reproducible research outcomes across different studies and species.
Optimizing primary sequences to enhance mRNA translation is an important focus in the development of mRNA-based therapeutics ( 27 ). Translation efficiency and ribosome pausing are known to be two critical factors influencing the dynamics of translation. In this update, we tackle these aspects in RPFdb v3.0, facilitating deeper insights into the intricacies of mRNA translation. We now present translation efficiency estimates by dividing the footprint RPKM by mRNA RPKM for each gene’s coding sequence, utilizing both Ribo-seq and RNA-seq data ( 4 ). This enables researchers to quantitatively assess the rate of mRNA translation into proteins, identifying genes with high translation activity and shedding light on the cellular mechanisms governing protein production. Additionally, we introduce context-specific pausing scores for each triplet amino acid (tri-AA). These scores, calculated as the sum of normalized ribosome densities on each tri-AA motif using RiboMiner software ( 28 ), are crucial for pinpointing tri-AA motifs with enhanced ribosome enrichment. Such motifs often signify regions where translation is temporarily halted or slowed, potentially influencing protein folding, localization or regulatory functions. These new features will improve our understanding of translational dynamics by elucidating where and how ribosomes regulate protein synthesis. Furthermore, Ribo-seq tracks coupled with RNA-seq tracks are currently available, enabling intuitive display of coverage signals over genomic ranges and supporting comparative analysis of translation rates. Potentially, this update has significant implications for developing RNA therapeutic strategies, such as aiding in the design of mRNA sequences with optimized translation rates and providing a basis for identifying and improving translational pause sites.
We have added a resource webpage to RPFdb v3.0 that serves as an information hub for researchers engaged in translatome studies, offering a concise yet informative summary of recent advancements in this rapidly evolving field. This curated collection highlights cutting-edge techniques that have revolutionized our ability to investigate translation at a genome-wide scale. Central to this resource is an overview of Ribo-seq and its variant methodologies, ranging from bulk profiling to single-cell profiling and spatial profiling. The page also features a section on computational tools specifically designed for Ribo-seq data analysis, covering software for read alignment, differential translation analysis and visualization of ribosome occupancy profiles, among others. By consolidating this information, we aim to equip researchers with essential knowledge to advance their translational research endeavors. This centralized resource not only facilitates easier access to cutting-edge methodologies but also promotes best practices in the field of translatome research.
The significant expansion in both datasets and content necessitated an enhanced web interface. To achieve easier navigation, we redesigned the study browse and sample browse pages, offering a more intuitive layout and improved user experience. Furthermore, we optimized the ORF search response on the ORF catalog page, significantly reducing wait times for users. Additionally, we introduced new dedicated pages for quantification content, including measurements of ribosome occupancy, translation efficiency and ribosome pausing. These separate pages streamline the processes of data retrieval, comparison and visualization, thereby enhancing researchers’ capability to derive meaningful insights efficiently. To facilitate secondary analyses of data, we also enhanced the download functionality. The download page now supports retrieval of translation efficiency, pausing score, Ribo-seq tracks and RNA-seq tracks. These improvements collectively aim to provide a more user-friendly and comprehensive platform for researchers engaged in translatome studies, supporting more efficient data access and analysis.
To access information about specific Ribo-seq data and its related content, users can start by navigating to the ‘Study browse’ page under the ‘Browse’ button on the homepage. For instance, entering the keyword ‘eye’ in the search box will return a dataset titled ‘Change in translation efficiency in mouse eyes at P0.5 by RNG140 knockout’. Clicking the ‘Details’ button will direct users to the ‘Sample browse’ page, which provides comprehensive meta information about the dataset, including sample attributes and experimental variables, quality control checks for raw sequence data and post-mapping data, mapping statistics for each sample and more. For this dataset, users can review actively translated ORFs on the ‘ORF catalog’ page, and quantitative measurements on the ‘Ribosome occupancy’, ‘Translation efficiency’ and ‘Ribosome pausing’ pages under the ‘Quantification’ button. Notably, the ‘Ribosome occupancy’ and ‘Translation efficiency’ pages allow users to retrieve individual gene information. For example, by selecting ‘M.musculus’ as the species and entering ‘Smad4 (a gene important in eye development and disease) as the gene of interest, users can compare results across different experimental conditions within the same species. The ‘Ribosome occupancy’ page also features a genome browser for visualizing Ribo-seq tracks, enabling users to examine the distribution of ribosomes along transcripts. All the quantitative measurements for this dataset can be downloaded from the ‘Download’ page, facilitating further analysis and integration with other data types. This example demonstrates how users can efficiently navigate the database to access, visualize and analyze Ribo-seq data relevant to their research interests.
The RPFdb database is dedicated to advancing research within the ribosome profiling community, providing a comprehensive platform to explore Ribo-seq data and related content across diverse species. The latest update to RPFdb has further enhanced its utility with expanded data content and improved functionality, facilitating more efficient and insightful analyses. Although RPFdb has made substantial strides in democratizing access to Ribo-seq data and related contents, continuous development and adaptation will be crucial to keep pace with the rapid evolution in the field of translatomics. As Ribo-seq technology continues to advance, particularly with the emergence of single-cell translatomics ( 29–31 ), RPFdb must adapt to accommodate these new data types. Including single-cell Ribo-seq data would allow researchers to explore translational heterogeneity, providing unprecedented insights into cell-specific translation and translational regulation. Moreover, integrating spatial Ribo-seq data could offer a new dimension to our understanding of localized translation within tissues. Additional development of RPFdb could focus on incorporating more sophisticated online analysis and visualization tools directly into the platform. This could include interactive data exploration features, allowing users to perform custom secondary analyses without the need for local computational resources. Advanced visualization tools could enable researchers to generate publication-quality figures directly from the web interface, enhancing the accessibility and interpretability of complex Ribo-seq data.
RPFdb is publicly available at http://www.rpfdb.org or http://sysbio.sysu.edu.cn/rpfdb/ .
We would like to thank all team members for their support and RPFdb users for their invaluable feedback and suggestions.
Author contributions : H.W. and Z.X.: conceptualization and writing; Y.W.: data collection, data analysis, writing and website redesign; Y.T.: data collection, data analysis and data presentation.
National Natural Science Foundation of China [32270700 to H.W.W., in part]; Guangdong Basic and Applied Basic Research Foundation [2024A1515010103 to H.W.W.]; Guangzhou Science and Technology Program key projects [2024A03J0158 to H.W.W.]. Funding for open access charge: National Natural Science Foundation of China.
Conflict of interest statement . None declared.
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Sell my car, car research, sign in, 2024 toyota land cruiser review and test drive.
The Land Cruiser returns as a smaller, less costly, retro-styled, and more utilitarian SUV.
QuickTakes:
Toyota's Land Cruiser debuted in the United States in 1958 as a basic four-wheel-drive , Jeep-like tool. By 2021, it had grown into a large, leather-lined, luxe SUV just shy of a Lexus badge and tickled the $90,000 mark in price. Given its origin story, that '21 Land Cruiser exemplified automotive mission creep. At the end of that year, Toyota shelved it — temporarily, as it turns out.
With the redesigned 2024 Land Cruiser, Toyota has returned to the drawing board. It's a more basic SUV with a robust four-wheel-drive system and a lower price tag. Like the previous Cruiser, it still has a Lexus cousin, but this time it's the GX . A Toyota-badged sibling arrives soon as the redesigned 2025 4Runner .
The new 2024 Toyota Land Cruiser answers to several market realities. First, the old Land Cruiser felt too bulky and luxurious, particularly given the existence of the nearly identical Lexus LX. Second, Jeep's perennially popular Wrangler , Ford's recently reintroduced Bronco , and Land Rover's well-received Defender shifted the segment toward more elemental off-roaders.
Third, in my opinion, the Land Cruiser name still has great value. Wasting it would be a shame.
The 2024 Toyota Land Cruiser comes in three trim levels. Toyota calls the base model 1958 (for the first year it sold the model in the U.S.), while the middle trim is simply called Land Cruiser and the top version is the First Edition.
Base prices range from the high $50,000s to the mid-$70,000s, including the destination charge to ship the SUV from the factory in Tokyo, Japan, to your local dealership.
For this Land Cruiser review, I test-drove the middle trim level variant in Arizona. Highlights from the optional equipment list include the Premium Package, 20-inch alloy wheels, a large roof rack, and white paint that nicely offset the Smoky Blue body color.
The manufacturer's suggested retail price of the test vehicle was $71,364, including the $1,395 destination charge. (The carmaker has since increased its destination charge to $1,450.) Toyota provided the vehicle for this Land Cruiser review.
The Land Cruiser isn't as distinctive as the Ford Bronco or Jeep Wrangler, instead presenting a more mature design. The round headlights on 1958 and First Edition models, the jaunty upkick at the rear door windows, and the available bright paint colors all add character, however.
High-grade interior plastics decorate the Land Cruiser's cabin, and the build quality is excellent. Some minor details are pleasing, too, such as the shape of the JBL audio system's tweeter housings.
That said, there's room for improvement. The rear seatbelts get in the way when you fold and tumble the second-row seats up and forward, for example. Also, the rear seats don't fold flat, so you can't create a flat-load floor in this SUV for cargo hauling or camping out in the back.
The new Land Cruiser isn't as posh as the old Land Cruiser, but it's not exactly lacking. Where the base Land Cruiser 1958 comes with cloth seats, the middle-trim Land Cruiser has SofTex artificial leather or, as an option, the real thing. My test vehicle's medium-brown leather upholstery looked terrific, adding a hint of richness to the cabin.
Thanks to the large center console, there's a cozy, tucked-in feeling up front. The only real letdown I found was that the passenger seat doesn't have the same manually adjustable thigh bolster as the driver's seat.
The rear-seat room felt about average, with just enough space for my legs and knees as long as the front seats weren't at the far end of their travel. There's also decent headroom. Given that the Land Cruiser is very tall, though, you might expect there'd be more.
The Land Cruiser does not offer a third-row seat, which surprised me, because the Lexus GX provides one.
Since it doesn't have a third-row seat, it seems like the new Land Cruiser should provide a generous cargo area. It's by no means tiny, measuring 37.5 cubic-feet behind the rear seats, but the high cargo floor dictated by the hybrid powertrain's battery means loading objects requires more effort than with other SUVs. The Land Cruiser's high ride height accentuates that, too.
The test vehicle had a refrigerated cooler box perfect for stashing a few soda cans or a box of chocolates. However, it takes the place of the center console storage bin, and I missed that storage space more than I liked the mini fridge.
Toyota equips the Land Cruiser with Toyota Audio Multimedia, the company's in-house infotainment system. The Land Cruiser 1958 includes an 8.0-inch touchscreen, but my midlevel test vehicle had a larger 12.3-inch display.
Wireless Apple CarPlay and Android Auto connectivity, SiriusXM satellite radio, and a 10-speaker sound system are standard. My test vehicle boosted that equation with an optional 14-speaker JBL audio package. This system performed exceptionally well, with excellent fidelity and strength in the bass department.
Connecting my iPhone via Bluetooth proved seamless and running CarPlay was no trouble. Upon returning to the vehicle, my device reconnected every time. The native voice recognition — alerted with a firm "Hey, Toyota" — could find tricky business names that sometimes flummox other systems. It also usefully notes whether a chosen business is open or closed at the time of the search.
The new Land Cruiser's instrument cluster is fully digital and configurable, offering detailed information that I found easy to reference. There are two options for presenting the instruments: conventional dial gauges or a simple slate of data.
My test vehicle's head-up display repeated the most vital information in my line of sight, including road speed, speed limit, and navigational graphics when active. As part of the optional Premium Package, a digital rearview camera mirror offers a clear view to the rear, so luggage stacked to the rafters inside the cargo area won't block the view.
Every 2024 Land Cruiser has Toyota Safety Sense 3.0 (TSS 3.0), a collection of advanced driver-assistance systems that equips the SUV with the features you likely expect in a modern vehicle.
On the freeway, the Land Cruiser's adaptive cruise control never failed to see a leading car slow down, nor did it take more than a split second to recognize a merging vehicle in front. The adaptive cruise also brought the SUV to a complete stop when the car ahead did the same. Once traffic started moving again, I could simply press the cruise control's resume function to let it accelerate again.
In addition, the Land Cruiser's lane-centering assist performed nearly flawlessly. It had one unusual tendency to hug a yellow line on the driver's side through a construction zone on a freeway I frequently drive. I didn't feel this was horrible, though, because hugging the other side would have meant kissing tractor-trailers, an activity I prefer to avoid.
Lane-change assist is also part of TSS 3.0, where a tip of the turn signal initiates a lane change if the coast is clear. Calibrated conservatively, it requires plenty of clearance ahead and behind. The system also takes longer to execute a lane change than most drivers, I found, but that's understandable. Overall, I found it too lethargic to use regularly.
At the heart of the new Land Cruiser is a hybrid powertrain based on a turbocharged 2.4-liter four-cylinder engine. It makes a healthy 326 horsepower and a whopping 465 pound-feet of torque, and while that's down in power from the old V8-powered 2021 Land Cruiser, torque is far more critical in a heavy vehicle.
Most SUVs (even those with fantastic off-roading capabilities) will see more suburban pavement than red rock-lined trails of the Wild West. Toyota fits the Land Cruiser with cushy suspension tuning, mild Dunlop Grandtrek mud and snow tires, and lots of noise-abating insulation. It all equates to a quiet ride in tame, suburban environments.
At 5,038 pounds, the Land Cruiser needs every bit of its 465 lb-ft of torque to get underway, and it does so smartly. This SUV isn't fast, but you can't complain about the acceleration. In the combustion world, a good V8 makes a glorious sound. What emanates from the new Cruiser's turbo hybrid four-cylinder can't match the old Cruiser's V8 voice, but it isn't rough, unrefined, or surly in the way some large-displacement fours can be.
The engine doles out power smoothly and controllably when off-roading, too. Throughout one afternoon in the dirty and rocky stuff, the Land Cruiser handled trails a bit beyond the scope of the standard tires, and the throttle's progressive nature proved spot-on for rough going. Disconnecting the front anti-roll bar (which I did via a button on the console) is probably overkill on anything but the ruttiest path, but I tried it out. It worked, and I harmed no wheels, running boards, or suspension links in the process.
The Land Cruiser wafts over highway pavement at least as well as it dispenses with rutty and rocky trails. The ride quality and impact harshness feel like what I might expect of a Lexus SUV, to a point.
The Toyota's truckier nature is evident on twisty roads. The grip is just middling, and there's lots of body lean in corners and nose-dive under braking. Actual braking power and effectiveness — separate from the body's reaction to brake application — is excellent, though.
At speeds above 75 mph, the Land Cruiser exhibits wind noise. However, this is inevitable given its tall stature, large side mirrors, and optional roof rack.
On my 73-mile loop of mixed freeway and suburban driving, the Land Cruiser logged a disappointing 20.5 mpg. It's disappointing because the EPA rates it at 22/25/23 mpg in city/highway/combined driving.
Worse, Toyota says the Land Cruiser is supposed to run on premium fuel. Between the observed fuel-economy shortfall and the extra cost of premium gas, owners may have to bear higher gas costs than anticipated.
Compared with Land Cruisers of the past 15 years, the more popular 4Runner exemplifies the truly mixed-use 4x4 with its excellent off-roading capabilities and reputation for reliability.
Some family friction is likely to ensue.
Looking beyond the Toyota lineup, Land Rover's compelling Defender 110 is in a similar price league and has the same general mission as the Land Cruiser. And the Jeep Grand Cherokee is generally acknowledged to have excellent off-roading ability, everyday practicality, and plenty of creature comforts.
Regardless, I imagine what matters most to the fans of the brand is that the Land Cruiser is back in business. Better yet, it is more faithful to its original mission than it has been in a long time.
Written by humans. Edited by humans.
From racing exotic sports cars, to ranking new cars, to peeling back layers of cover up in an exhaust emissions scandal, Jim has chronicled the automotive sector for decades. Jim has also worked inside the corporate headquarters of three carmakers, and therefore understands how the automotive sausage is really made. But Jim’s affinity for vehicles takes a back seat to finding the truth and the cultural implications of modern transportation. He has also lectured at universities to engineering and policy students and faculty on the industry’s relationship with legislation in the wake of the diesel exhaust emissions scandal several years ago. Put simply, Jim reports on autos, mobility, tech, car culture, and the traffic jam of topics within.
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The amount of betting adverts, including pitchside hoardings and shirt logos, almost trebled during the opening weekend of the Premier League season compared to last year, new research says.
Research methods are specific procedures for collecting and analyzing data. Developing your research methods is an integral part of your research design. When planning your methods, there are two key decisions you will make. First, decide how you will collect data. Your methods depend on what type of data you need to answer your research question:
The progression from RPFdb v1.0 to v3.0 demonstrates consistent and substantial growth. Each version has markedly increased the number of samples, studies and species represented. Notably, the latest version nearly doubles the Ribo-seq datasets compared with v2.0 and represents more than a 6-fold increase from v1.0.
The Open access journal Research, published in association with CAST, publishes innovative, wide-ranging research in life sciences, physical sciences, engineering and applied science. ... P = 0.0419). Conclusion: Overall, the blind nasopharyngeal brushing diagnostic method, combining EBV and host methylation markers, showed great potential in ...
Toyota equips the Land Cruiser with Toyota Audio Multimedia, the company's in-house infotainment system. The Land Cruiser 1958 includes an 8.0-inch touchscreen, but my midlevel test vehicle had a larger 12.3-inch display. Wireless Apple CarPlay and Android Auto connectivity, SiriusXM satellite radio, and a 10-speaker sound system are standard ...