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Hi all,
If we do not have anybody to do quality assurance (QA) of a large number of papers that we get from database searches, say, for example, about a 1000 papers, for a review paper, then what should one do?
The PRISMA guideline mentions that a second person should review the papers that are included into a review paper (scoping or systematic, etc), but if we do not have anybody to review this large number of papers (for example, 1000 papers) for eligibility, then what should be done? Please help.
Thanks
Kind Regards,
Zakia Salod
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Why don't you collaborate with an epidemiologist? Even if you have 1000 article to be included in your study, you want to extract data, yes? So, it would be possible for checking the quality just like extraction. In addition, collaborating with an epidemiologist will make your article so valuable and this is the important thing about an article. Good luck
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I am looking to recover all proteins that are shared (e.g., to sequence similarity of 50%) between two species (e.g., Nicotiana tabacum and Arabidopsis thaliana). Is there a way to use UniProt's search tool to do this systematically? Alternatively, are there any better databases for this?
Thanks in advance for any advice!
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You could start from there or could ask the questions. Good luck.
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  1. Which database is more preffered?
  2. How do you make your search term generate more papers?
  3. How do you set your boundaries?
  4. What other things needs consideration?
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A rapid review (or rapid evidence assessment) is a variation of a systematic review that balances time constraints with considerations in bias.
Step 1: Form/refine Question. ...
Step 2: Define Parameters. ...
Step 3: Identify Biases. ...
Step 4: Plan & Execute Search. ...
Step 5: Screen & Select. ...
Step 6: Quality Appraisal.
More items...•May 5, 2021
Rapid Review Protocol - Research Guides - Virginia Commonwealth ...
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One question related to science database search. I want to search SCI database to verify if paper is indexed or not. I searched through web of science, and as result I get one of my paper but does this mean that it s indexed in SCI database? thx, any comments are welcome.
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The Science Citation Index is accessed through the Web of Science platform, with which more databases can be searched simultaneously. To search the Science Citation Index individually use the More Settings option at the foot of the Web of Science search screen.
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Whenever researchers start with evidence-based reviews, whether they are scoping, rapid reviews, systematic reviews, or even current form of narrative reviews, they face problems at every steps which require assistance from people who have already been doing these kind of reviews. These problems can range from topic selection, to team formation to database search to registration and many more. Here I would like to initiate a discussion to identify the problems
faced by each and every researcher who is either planning to start or is currently doing reviews and welcome views to look for solutions for these problems with a collective approach.
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One of the most common problems encountered is the lack of randomized controlled clinical trials and the heterogeneity of the statistical analysis. These create an issue when performing meta analysis on the included studies. Please find the systematic review reference below from our group.
Gandhi V, Mehta S, Gauthier M, et al. Comparison of external apical root resorption with clear aligners and pre-adjusted edgewise appliances in non-extraction cases: a systematic review and meta-analysis. Eur J Orthod. 2021;43(1):15-24. doi:10.1093/ejo/cjaa013
Abu Arqub S, Mehta S, Iverson MG, Yadav S, Upadhyay M, Almuzian M. Does Mini Screw Assisted Rapid Palatal Expansion (MARPE) have an influence on airway and breathing in middle-aged children and adolescents? A systematic review. Int Orthod. 2021;19(1):37-50. doi:10.1016/j.ortho.2021.01.004
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The Mercator Institute for Literacy and Language Education at the University of Cologne, Germany, is conducting a systematic review on the effectiveness of language integrated strategies (e.g. scaffolding, Sheltered Instruction Observation Protocol (SIOP)) in classrooms. In this review, it is intended to collate, critically appraise and synthesize existing research evidence according to pre-defined criteria.
To complement our electronic database search, we are looking for manuscripts/working papers/project reports/dissertations (except for BA-/MA-thesis) that have not (yet) been published or submitted for publication (and are not (yet) indexed in databases).
We are interested in (quasi-)experimental and observational studies using a control group design that (statistically) examine
  • the effectiveness of concepts of instruction that integrate language support and subject teaching
  • for children of primary or secondary school age.
If you have carried out this type of study or if first results of an ongoing study are available, we would like to kindly request the document. Submitted studies will be reviewed by the project team; studies that match the review inclusion criteria will be included in the final review synthesis (i.e. summarized and discussed). Publication of the results is planned for 2021.
Of course, your submissions will only be used within the scope of the review and will not be passed to third parties.
Please send documents by September 30th, 2019 to Leonie Twente at leonie.twente@mercator.uni-koeln.de. If you have any questions, please contact Till Woerfel at till.woerfel@mercator.uni-koeln.de. Alternatively you can use the comment field below.
Thank you for your support!
Kind regards,
Till Woerfel, Martha Höfler, Annika Witte, Anastasia Knaus, Rebekka Wanka and Leonie Twente
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I'm conducting a systematic literature review about people's pro-environmental behaviour. I'm using Scopus and Google Scholar as my academic databases for searching peer-reviewed articles. Wondering if the two databases are enough or I should add other databases as well? Interestingly, I noticed that most of the papers I found in Web of Science are already included in Scopus too but not vice versa. Any advice or comments appreciated.
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Hi! Concerning the question which search system best fits for a systematic review I can contribute a paper we just recently published. It analysies 28 search engines and bibliographic databases on their suitability for systematic reviews:
Hope this helps.
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Dear Colleagues, We are currently conducting a meta-analysis on sex-specific genetic variances of fitness components. Specifically, we aim to test whether additive genetic variances of reproductive success (and other fitness correlates) differ between males and females. Because meta-analyses are often sensitive to publication bias, we are looking for unpublished datasets that quantified genetic variances of both sexes within the same experimental setup or field population. Ideally, the data should include sample size, mean estimate, unstandardized genetic variance, coefficient of variation, and heritability estimates for both sexes. If you have, or know of, such unpublished data sets, we would love to hear about it. Moreover, we would be very grateful if you could point us to published work that provides this type of information but may go unnoticed in database searches applying search terms like ‘genetic variation’, ‘heritability’ and ‘reproductive success’. Please email suggestions or questions to: janicke.tim@gmail.com Many, many thanks in advance! Tim Janicke (CEFE-CNRS, Montpellier) with Lennart Winkler (Technische Universitaet Dresden) Maria Moiron (CEFE-CNRS, Montpellier) Ted Morrow (University of Sussex)
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I will share this with my colleagues who may help, with best wishes,
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I have several pathways and want to know the biological process and metabolism related to each pathway.
Is there any database to search them?
For example I want to know the DRUG METABOLISM CYTOCHROME P450 pathway involved in what biological mechanisms or process?
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If you know your species, then Biocyc would be my suggestion. You can select your species and strain, and then do a search for compounds in your pathway, followed by looking at what process it is involved in. If do not know you're organism, you can use Metacyc. Some other databases are KEGG, EAWAG, Uniprot.
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I have undertaken a database search and identified the articles. I would like to evaluate the effectiveness of this search. Does the number of included studied identified by both databases count?
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According to this study of Bramer WM et al. ( ), which investigates the actual retrieval from the original searches for systematic reviews, a combination of Embase, MEDLINE, Web of ScienceCore Collection, and Google Scholar databases was found to perform best (overall recall of 98.3 and 100% recall in 72% of systematic reviews). These findings suggest that optimal searches in systematic reviews should search at least Embase, MEDLINE, Web of Science, and Google Scholar as a minimum requirement to guarantee adequate and efficient coverage.
Some extra databases apart from Embase, MEDLINE, Web of ScienceCore Collection and Google Scholar are:
  • Cochrane Library (Includes the Cochrane Central Register of Controlled Trials)
  • Cochrane Central (contains MEDLINE trials plus many trials from other, non-indexed sources; limited to randomized and randomized controlled trials. )
  • ClinicalTrials.gov (Registers trials that are recruiting and reports which have been completed. Since a majority of the trials in this registry are never published, you'll need to search here if you're looking or clinical trial data.)
Having said that, a combination of databases seems to bring the best results.
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I'm interested in identifying proteins from egg whites through LC-MS and MALDI-TOF, then through database searching. The protocol that I was reading requires dialysis. Can I opt for centrifugation instead?
Thanks
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There is a 'common method' to use a sucrose gradient in centrifugation (developed in the 1970's) to separate proteins by molecular weight. I have no idea whether it will work on egg proteins.
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Please suggestions about finding numbers (statistics, figures) about a certain topic that you have in mind but not if the numbers are available. For example, number of hours people spend deliberating about which career to choose vs the number of hours doing that career. Or number of hours people spend deliberating about which career to choose vs number of hours doing they deliberate for much much less important decisions like what clothes they should buy?How do I find numbers related to career deliberation? Both tips about the general "number finding" issue and the specific "career deliberation" issue are appreciated .
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email response from Paul Bradshaw (Birmingham uni) of onlinejournalismblog.com: " Hi Hashem, this is quite a broad question and so the answer is hard to give. There are many ways to find statistics/figures – for example using advanced search operators like site:ac.uk or filetype:xlsx will help you narrow your search, or specialist search engines like Zanran (which you mention) which focus on tables and charts. You can also try a two-step approach by first searching for organisations which are likely to collect that information (governmental, charities, academic, survey companies) and then approaching them. More broadly you can look at a system and identify which organisations collect which information within that system (e.g. Regulators do inspections, using gov.uk etc) In the specific example of career deliberation you may be best trying the two-step approach. It may be that recruitment companies have commissioned research of this type before, or you can access polling companies to find out if they’ve done anything on this.
Thanks,
Paul Bradshaw"
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Can anyone with CSD access help me with a following cell parameter if any structure exists:
a=11.18Å, α=81.97°, V=2191 Å,
b=12.63 Å, β=71.80°, Triclinic P
c=17.79 Å γ=66.71°
Thanks in advance!
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Many many thanks Dr. Daniel.
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I have performed LC MS/MS analysis of pooled patients' plasma and have identified one protein of interest. The database search of the MS/MS spectrum was performed with proteome discoverer software. The identified protein of interest after database search gave a score of 4.5 and number of unique peptide identified is 1. Can I report the protein based on such a result? Any reference link will be of great help where such situations are reported and validated.
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I have few more queries before answering. I want to know which search algorithm did you use for this analysis. Is it Sequest (which i think it is) or Mascot?
If using Sequest, the score you talking about is called Xcorr for which 4.5 is good. But in addition to this, one must also see how many Peptide spectrum matches (PSMs) are observed for that particular peptide belonging to your protein of interest. One must also open the spectra file to see the assignement of the b- and y-ions to confirm the same.
Thank you!
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I am working on a project examining teacher's role in supporting student SRL. This clearly can include many things such as implementing interventions, utilizing teaching practices to foster or teach SRL skills (e.g., provide effective feedback, engage students in self-assessment), designing effective assignments (e.g., open-ended, long term projects), and creating supportive learning environments. I have read some really great review papers and many manuscripts, but my database searches seem to miss the mark (likely due to terminology) and I feel as though I am missing something. I am early in this project and if you know of any resources you think that I might want to read or include as I work on this project, I welcome your suggestions. Thanks a lot!
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Thanks for the recommendation. I will look into it
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Hello everyone, Need a bit of help in google scholar, Indmed and Latin LILAC search database.
thank you
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Put Pneumonia in the "all of the words category", and child infant neonate in the "at least one of the words" category.
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I plan to perform systematic review and I need to establish databases that will be searched for. I found that majority of researchers screen for two databases (PubMed and Medline). According to NIH website PubMed gives more results and additionally includes those from Medline:
The question is whether it makes sense to search for Medline database?
Best,
Wacław
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hello
In addition to PubMed, you can also access MEDLINE through an EBSCO interface and an ISI interface. All of them access the same database (MEDLINE), but each has different capabilites, and will provide a different user experience. In other words, "PubMed is one way to access MEDLINE."
regards
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I need to search the NCI database and i can only find the MiniMayBridge and the sample satabases and can't find the option to browse and search other databases. I'm using Discovery studio 2.5.5. thank you
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May be this document will help you.
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as i know inverted index consist of keywords and the document identifiers contain this keyword and the search on this index structure is sequential for single keyword search but if i want to search for multi keyword in this index . will divide this multi keyword for single keywords and search for it sequentially . iam thinking to use map-reduce algorithm to make this search in parallel.
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You use MapReduce to build the index and then efficiently query it.Querying the index is commonly NOT implemented in the MapReduce Paradigm since it's too slow and not suited for that.
You can also use ElasticSearch https://www.elastic.co/ to take care of all of this.
For a collection of 1500 documents, every decent index will work, it's not a lot of data.
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other than contents ... how to evaluate a database as appropriate or not ?
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thank you all, great and helpful bits of advice!
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if it is possible please suggest me methods to optimize the database connections of a particular website 
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It depends on the database itself. In software development particularly web application, you can't have optimised database straight away. Off course, the normal practices should be applied and the database should be optimised as it has to, but what I have learnt, some of the attributes of various tables are differently manipulated to that when it was designed. It is always a good idea to revisit most of the database as there is always a scope for improvement. 
Coming back to your question, more detail is required to get a precise response.
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Are there any values/references for how low/high the False discovery rate should/can be? For example, using Mascot search with the automatic decoy database for small to medium sized samples (100-10,000 MS/MS scans). The sample is searched e.g with all entries using SwissProt. The FDR is set by default to 5% (significant threshold). The automatic decoy database is also searched with all entries using SwissProt. How low/high can the FDR for the decoy database can be? For the small to medium sized samples, I obtain values from 20-80% FDR in the decoy base, which seems relatively high to me. How big has a sample to be that a decoy database search is required in MS/MS scan numbers? What makes a sample small, medium and big? Thanks for your help in this matter, Martina
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The terms large and small are relative and relative to the process. Determination of large and small requires an understanding of the process. Your original concern was the false positive rate. The false positive rate of a process is the confirmed false positive rate. Example: A saliva test is devised to determine a blood-borne pathogen. The test is performed on individuals who have had definitive diagnoses by another means. The saliva test results are compared and the number of false positives and false negatives are determined.
Your interest is in setting a false positive rate. The usual method is to perform an uncertainty analysis and determine the distribution of measurement parameters. The cutoff for identification is set at 5% of the noise distribution. The cutoff is correct as long as the measurement distribution does not change.
Another method of setting the false positive rate is to adjust instrument or process parameters until a 5% rate is obtained. The setting is valid as long as adjustable parameters remain the same and the initial assumptions are sufficient and valid.
Why set a 5% false positive rate? The only reason is cost, tangible and intangible. Best would be zero false and negative results. The acceptable fraction of false positives should be established on a cost-benefit basis, not at 5% because everybody does it.
How do we determine what is a large and small sample? Samples are large or small based on cost-benefit and difficulty of obtaining the answer required.
Assume you have a system population with fixed characteristics. Fixed characteristics means that characteristics vary among individuals, but no individual varies. A given characteristic might have a large or small standard deviation. The larger the sample, the smaller the standard error of the characteristic. A characteristic with a small standard deviation might reach an acceptable standard error with fewer samples than one with a larger standard deviation. The important factor is 'acceptable.' A narrow acceptable range will require more samples than a wide acceptable range. The definition of large or small sample size will depend on the difficulty of meeting the requirements and the cost of meeting the requirements.
Assume you have a system population with variable characteristics, meaning, characteristics vary among individuals and each individual is variable. Measurement of a characteristic for each individual might depend on when the measurement was made. The standard error will not depend, only, on the sample number and may converge to a fixed value after a given sample size. Large and small sample size relative to the convergence will have a different relationship.
Sample size might be augmented by other statistical, numerical, or grouping techniques. The efficacy of these techniques will depend upon structural characteristics of the population.
Many guides and regulations specify statistical limits and requirements such as false positive rates. These specifications may apply in some cases, but are often purely arbitrary and based on convention. It is necessary to investigate each situation for question asked, data and population structure, and what is necessary to answer the question based on the needs of the question.
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Is there a way to search in the Acknowledgements field of “all” published scientific papers? I can’t find such a delimiter in Web of Science (but maybe I just don’t know where to find it). Do you know of any other database / search engine that will let me do this?
I'm looking to quantify the use of various words and phrases.
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Can someone direct me to sample quantitative data sets that can be used to teach simple descriptive statistics in an online course?
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R package has several
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Hi, 
I am looking to explore the association of  genes with clinical outcome, 
I tried a bit the Oncomine site, however I will be happy to know about alternatives.
Thanks, Ran
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Thanks for both. 
Norman, I think that the CBioportal is probably the one I looked for. 
Thanks, Ran
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It is known that cancers are associated with translocations of different chromosomal arms.I want to find epigenetic marks like histone methylations,acetylations, DNA methylations etc in fusion gene products. I have tried searching UCSC genome browser but no luck yet.
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you can find a list with many databases and what they offer here http://epigenie.com/epigenetic-tools-and-databases/ . Hope you can find what you need!
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I am working on detecting different compounds present in my sample. I ran in using LC-MS (Agilent QtoF). I am only used to use Metlin as my database for searching compounds using my m/z. But now I also have to search for any toxic compounds. Is there other database that may be useful regarding this matter?
Thanks
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Hi Carl Angelo, I am just reading your question and are you sure  that you intend to search for inorganic compounds in your LC-MS data?
If yes, then Metlin is definitely not the right database and the method that you are using for analyses as well. Additionally searching the database only using accurate mass is not great as it will not give you any level of confidence that the compound you picked from the library is the right one. You should definitely consider MS/MS experiments, there are also other free (for example Mass Bank) and paid libraries of MSMS data (for example ForensixTox from Agilent available that could help you with your work.
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I have a database with millions of records stored in it. I want to implement Search and Functionalists in My db with some AI and data mining techniques and methods.
Suggest me Some Algo, Methods and  Techniques for implementing this with AI. So that it becomes more and more efficient as the time passes.
It would be nice if anyone suggest with keep in mind that I am working with Python Frameworks and PHP.
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YOU CAN USE WEKA AND RAPID MINER TOOLS. THEY HAVE GOT VERY RICH FUNCTIONALITY FOR ALL THESE TASKS.
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1. co-occurrence of two words
2. co-occurrence of document and words
Do algorithms work on these two concepts?
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Co-occurrence of words with documents can also be used as a measure for semantic similarity. This was done, for example, in Explicit Semantic Analysis (ESA), http://www.cs.technion.ac.il/~gabr/resources/code/esa/esa.html
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I am interested in detection of all protein isoforms arising from alternative splicing events. To do this, I would like to set up database searches to account for all isoforms by parsing unique peptides separately from razor peptides common to 2 or more isoforms. In the end it would result in separate protein assignments for unique isoforms and for common isoforms. Does anyone do this already, and if so, is there a way to set database search parameters in such a way as to do this quantitatively, i.e. unique isoform 1 protein ratio, unique isoform 2 protein ratio, protein ratio arising from common peptide isoforms 1 and 2, etc.? Even standard parsimony assumptions do not always result in what I consider accurate protein ratios. For instance, looking at a protein where isoform 2 is subsumed by isoform 1 I've detected isoform 1 unique peptides at one ratio and common 1/2 peptides at a very different ratio. By standard parsimony I would conclude that only 1 is present, but by the peptide ratios it is clear that 2 is also present but at a very different ratio than isoform 1. I've read several papers touching on these issues, but haven't yet found anything that fully addresses them.
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Identifying and quantifying multiple protein isoforms is best accomplished by setting up an MRM approach, where you use heavy standards of each isoform to establish your assay and then measure your samples.
For the reasons you mention in your question, I do not think that a non-targeted approach will give you the results you seek.
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I'd like to have it for my article.
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Dear Shima,
have you search the OECD Library?  http://www.oecd-ilibrary.org/   It requires a subscription.
You can search the topic on Google Scholar. It's free and it retrieves a lot of results. Search also on the World Bank database; http://data.worldbank.org/
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Hi to all. I do not have an ESI-MS coupled to an hplc, and I need to analyze a band excised from a gel. Once I have desalted the tryptic digest, how can I set the database search considering that tryptic peptides have a +2 or +3 charge states? In MASCOT (Matrix science) I have only the possibility to perform research of peptide mass finger printing setting MH+ charge states, and to perform a search against MS/MS data.
Thank you
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Hi Antonio,
to search for +2 and +3 charged molecules is not simple, you have to deconvolute the spectrum first - for my knowledge, Agilent ofers a deconvolution software to create the "perfect" [M+H]+ spectrum, but other companies may offer such sofware, too. Second possibility: manual deconvolution of the most intesive signals, but this may consume tons of time... just search for Isotopic patterns with differences of 0.5 m/z or 0.33 m/z between the C12/C13 isotopes (if you have a signal of e.g. 1000, 1000.33, 1000.66 etc... this corresponds to a [M+3H]3+ ions with zero, one, or more C13 containing isotopes. The "deconvoluted" signal would be 2998, 2999 and 3000..., respectively. Calculate: [M+3H]3+ = 1000 m/z, [M+3H]+ = 3000 m/z, [M+H]+ = 2998 m/z. The molecule has the monoisotopic mass of 2997 in this case).
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I see a considerable convergence in database searching. Some papers reported they searched for example Pubmed, Scopus and Embase. Others said Scopus covers Medline, and it is not unnecessary to search Pubmed. I saw some papers reported they searched above databases together with web of science.
I would like to know which databases I should search with least overlapping results.
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thank you Shawn
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How to determine whether the entire search process, starting with the initial interview, can or should be improved.
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Hi Helen, I think the answer is to ask the clients how they experienced the process and the value of the search results to them. After all its all about delivery in the end. Moving into Health Librarianship from Higher Education I have noticed a shift from Customer Satisfaction (HE) to Impact (Health Librarianship). There are a whole series of tools here [ http://www.libraryservices.nhs.uk/forlibrarystaff/impactassessment/ ].