Submission & Publication process

 

Submission & Publication process

 A simplified view of important stages and roles in the publishing process of journal papers is given in the activity diagram in Figure 3.

The first step is to be taken by the author. After choosing an appropriate journal for submission, the author has to submit the paper according to the instructions issued by the journal editor. Most journals today offer the opportunity to submit the paper via the journal’s web site or a submission management system. At this stage, it is very important that the author follows the instructions, because submitted papers that do not adhere to the instructions can be rejected without taking into account the paper’s actual content.

Some common authors’ mistakes at this stage include:

 not adhering to the journal’s paper formatting and layout guidelines (e.g. using the wrong font size, line spacing, page numbering, referencing style, figure and table placement and visual guidelines);

 exceeding maximum paper length (word count, page count);

 the paper’s thematic focus not being within the scope of the journal’s subject areas.

If any of the above is evident when the editor does the preliminary review, the paper is likely to be immediately rejected regardless of its scientific contribution and quality. On the other hand, if these conditions are met, the paper will be considered for publication. The submitting author is notified of either one of these decisions.

The next step the editor takes is to select reviewers for peer reviewing the paper. The number of reviewers involved in the review process may vary from journal to journal, but usually the editor forwards the paper to at least three reviewers who are experts in the topic that is covered by the paper. Besides making comments and suggestions for improvements to the authors, reviewers generally support the editor in making a decision by providing information on the following general issues, which may vary in importance among different journals:

 thematic relevance to the journal’s scope of subjects;

 significance of contribution (does the paper contribute new findings to the body of knowledge in the field?);

 originality of the work (is similar research already published elsewhere?);

 coverage of relevant literature (did the authors report related work?).

Focusing more on the writing style of the paper, the following aspects are relevant to reviewers and might influence their recommended decision:

 clarity of writing: readability, organisation, conciseness and technical quality of the paper;

 appropriate title and abstract;

 appropriate use of well-designed figures and tables;

 sound conclusion and discussion;

 length of the paper relative to its usefulness.

Also increasing the likelihood of acceptance are the following characteristics of submitted papers:

 strong reputation of the author;

 successful test of the proposed theory;

 different content from that usually published in the journal.

 

When the assigned reviewers have finished reviewing and commenting the paper, the editor collects their recommendations and makes a decision which is sent to the corresponding author, who is indicated in the submitted manuscript. Generally, the notification by the editor will carry one of the following messages:

 

Accept. The paper is accepted as it was submitted. The paper will be published in one of the journal’s forthcoming issues. This outcome is very unlikely upon initial submission. Only in very rare cases will the paper be accepted right away. It is more likely that the paper has to be revised.

Revision. The editor requests a revision of (certain parts of) the paper. The authors have to modify the paper according to the suggestions and comments of the reviewers and the editor in order to be further considered for publication. After revising the paper accordingly, the author may submit the revised manuscript to the editor. This typically requires the authors to enclose a letter to the editor where they outline in detail how the reviewer and editorial comments were addressed in the revised version. After receiving the revised version, the editor either makes an accept/reject recommendation or, if required, forwards the paper for another round of reviewing, which usually involves those reviewers who were most critical about the original submission.

Reject. The editor does not see any chance for the paper to be published in the journal. This is the most frequent outcome of the review process of a journal. The editor usually encloses the reviewer comments. Typically, one or more reviewers

 had serious objections to one of the preconditions relevant to reviewers mentioned above

 found the paper to be out of the journal’s scope, lacking relevance or significance

 found fundamental flaws in the paper’s argument, data or methodology

 did not see any improvement with regard to previous submissions of the same paper.

If a revision is required and the author feels unable to comply with the editor’s recommendations, the author may either inform the editor about the disagreement or, alternatively, the paper may be sent to another appropriate journal in the field. The same applies to rejected papers.

The publisher typesets the paper and returns it as “galley proof” to the author, sometimes by way of the journal’s editor, who may also check the proof. “Galley proof” originally was the name for a typeset copy of a document used to permit correction of errors before the type was made up in pages; its name comes from the galley, a tray for holding composed type. With computerized typesetting, the term is also used as a synonym for “page proof” that shows how the made-up pages will appear. Various other paperwork may also appear at this time. Generally the publisher includes an order form for the author to order reprints of the article.  Author reprints are an exact replica of the article as it appears in the published journal, with a title-page cover included.

·       Reprints (Hard-copy reprints) – Reproductions of original journal articles and book chapters printed on high-quality paper. Reprints are available in color or black and white

·       E-Prints (Electronic reprints) – ePrints are encrypted, electronic copies of works in PDF format that you can distribute via email, post on a website or use in e-detailing

 If page charges are journal policy, the author receives a bill or invoice for the number of printed pages with the galley proof. Many journals require authors to execute a copyright release form, and such forms are often also enclosed with the galley. In addition to your signature as corresponding author, they may need to be signed by all co-authors.

As the final step in the publication process, the editor organizes and makes up an issue from proofed papers, and sends the entire issue to the publisher. The publisher then prints and mails the issue to journal subscribers. Reprints are usually mailed to authors within a week or two of publication.

Figure 1 Simplified activity diagram of the process of publishing a paper in a journal

 

Plagiarism

 

1.       Introducion

The term is Plagiarism (“plagiary”) derived from the Latin word ‘‘Plagiarius’’which means a “kidnapper” and it was first described in literature by the dramatist Ben Jonson in 1601 to describe literary theft. Despite all the strict, stringent, detailed and open instructions for researchers worldwide, there are occasional instances of dishonesty regarding research publications.

Merriam–Webster dictionary defines plagiarism as (a) The theft and use of other people's ideas or words as yours; b) Use of sources without attribution; c) Literary theft and d) presenting some ideas as own and as new, while this idea already exists in other source.

The first attempt to address plagiarism was in 1992 in the USA by the Office of Research Integrity (ORI) and then later in 1997 in the UK by Committee on Publication Ethics (COPE) both of which gave guidelines for research, scientific integrity and a set of principles to detect and present plagiarism.

2.       Types of plagiarism:

Plagiarism can be classified in many ways.

2.1.         Intentional and Unintentional Plagiarism

Also called Deliberate & Accidental Plagiarism. These two forms of plagiarism are differentiated based on degree of seriousness of the issue. Where, accidental plagiarism is considered to be of less severity and can be forgiven without giving harsh punishments, the same is not true for deliberate form of plagiarism. But most of the times, it is very difficult to rule out the possibilities and identify what form of plagiarism was performed.

2.1.1.     Intentional or Deliberate plagiarism occurs when the author deliberately, intentionally or knowingly copies entire text, paragraph or data and presents as its own. When a person is fully aware of copying the material or buying material from other sources and not giving credit to the source of origin, then such an act falls under the category of deliberate plagiarism. There are various examples of intentional plagiarism. For example, if a person buys someone else's work, copies material from the pre-published sources (in print or online), etc. If a person employs another person to write a study paper for them on their behalf and then present it as their own, then this is considered intentional plagiarism too. Another example is, where a person copies a material from its original source and then ask another person to translate it in his/her own words.

2.1.2.     Unintentional or Accidental Plagiarism occurs when the author either is not aware of such research, is unaware of the ethics in writing or does not know how to cite and thus presents similar articles. Sometimes, the students are naïve and are aware of the rules and guidelines of avoiding plagiarism. They are not educated about the proper ways of citing materials and are always in doubt while referencing material. Moreover, because of this doubtful situation, the students skip the step of citations. Hence, they fall prey to plagiarism. To avoid such situations, both the teachers and the students should learn to bridge this gap by communicating.

2.2.  Text/words Plagiarism or Direct Plagiarism

The commonest form of plagiarism is of text is known as “copy-cut-paste” or “word-to-word” writing wherein complete sentences, paragraph, tables or even pictures are reproduced from the original text without change and without proper acknowledgement and citation. Described as “…copying a portion of text from another source without giving credit to its author and without enclosing the borrowed text in quotation marks.” Earlier, plagiarizing text from an article also required considerable hard work as access to resources was limited. Today, with the advancement of technology, plagiarism is effortless. Because the information is easily available online and can then be copied.  With use of computers and the internet this form of plagiarism is very prevalent.

2.3.   Ideas/data Plagiarism

If a person came up with a new and unique idea, concept or problem to a solution, then it belongs to him or her. If any other person uses that particular idea or concept in his/her study and fails to acknowledge its true source of origin or acknowledge the person who came up with this innovative idea, then that person is committing plagiarism and it is part of academic distrust, breach of confidentiality and deceitful act. Copying of ideas is a common form of plagiarism wherein someone else’s ideas, presentations, audio or video files, thoughts, inferences or suggestions are made into research and presented as own without proper acknowledgement. This is of course very difficult to detect or prove. Some other methods are taking ideas from books, previously published thesis, journals, magazines, conferences or meetings.

2.4.      Source Plagiarism

This type of plagiarism uses previous article’s citations without actually reading or cross referencing the bibliography.

2.5.      Mosaic/patch writing

This happens when a new author uses the previous article text by replacing, reordering or rephrasing the words or sentences to give it new look without acknowledging the original author. It is also referred to as patch writing, in which the original structure of the sentence remains the same. This is a more common form of plagiarism. The sentence or paragraph structure is almost similar to the original source with a few words and phrases here and there. When the original author is not acknowledged and the reference not cited properly, such interlacing amounts to plagiarism.

2.6.      Self-Plagiarism

When everyone talks about stealing from other's work and ideas, it becomes difficult to believe that one can steal from himself/herself. Self-plagiarism happens when the author has added research on a previously published article, book, contributed chapter, journal, and presents it as a new without acknowledging the first article or taking permission from the previous publisher. Therefore, a copyright law has much importance and it and the Copyright law (the legal perspective) prevents the re-use of any “original work of authorship from any tangible medium of expression” (one's own or anyone else's) without the explicit permission of the copyright holder. Submission of the same article to multiple journals to increase the chances of publication or making multiple articles from a single article, known as, “salami slicing” is another form of plagiarism.

2.7.   Ghost writing

In this type the main contributor is not given due acknowledgement or someone who has not contributed is given due credit.

2.8.   Collusional

In this type the author asks a professional agent or institution to write an article and then claims as its own.

3.       Reasons for plagiarism

There are many reasons for plagiarism. An inherent desire or urge to be successful, cultural, psychological, aggressive nature towards success, fear of discrimination or failure, promotion, financial or job gains, peer pressure and need to increase one’s record number of publications are some of the individual causes for plagiarism. Lack of education at the undergraduate level regarding plagiarism is other reason for this trend. The demand of publication during interviews are also another cause for plagiarism. To get university or research grants, incentives from pharmaceutical companies, increase the academic and social performance of the department, gain access to international research, aim of publishing in indexed journals, unwillingness to work because of laziness among students while writing dissertation are other causes at institutional level. Shortage of time, inadequate preparation, poor English or writing skills and the pressure to publish more articles than to consider the quality, in shorter time are other causes for plagiarism.

4.       Detection of Plagiarism

Previously the only method to detect plagiarism was the ability/experience of the editor or reviewer to detect copies from the original. This involved extensive study of the literature, experience of the patterns of writing styles of different authors and cross checking them. In todays world there are many software and websites that help in detecting plagiarism .

Egs: Cross Check™, WCopyFind™, SafeAssign™, eTBLAST,

Viper (http://www.scanmyessay.com/plagiarism - free software)

5.       Principles to avoid plagiarism

The copyright laws were formed by the court of law to protect the privacy and integrity of someone's personal and intellectual property. Such laws, not only protected the published, written form of work, but also, media, photography, music, films and all other possible sources of information.

To avoid plagiarism, following things should be taken care.

Acknowledging online sources: If we take information from the internet or the writing is inspired by internet sources, then such sources should be acknowledged.

Use of quotation marks & references: Correct and proper use of references is very crucial in avoiding plagiarism. If the paper, article or study includes words or statements used by another person in his/her own study, then such statements should be properly quoted with the use of quotation marks and the paper should provide correct references too.

No paraphrasing: A writer must refrain him/herself from paraphrasing other people's work and is prohibited in claiming such work as a piece of his/her original product.

Acknowledgment: Correct and proper citation is mandatory to avoid plagiarism and give rightful credits to its original owner. If a person fails to cite his work properly, then it is considered plagiarism and the person is punishable according to the laws of that particular institution/state/government.

 

Reference

1.       Randhawa RK, Gupta N, Arora V, Nishant, Gupta P, 2015. Plagiarism: An Academic Dishonesty! J Updates Dent; 4(1):19-23.

2.       Yam Bahadur Roka, 2017. Plagiarism: Types, Causes and How to Avoid This Worldwide Problem, Nepal Journal of Neuroscience, 14 (3): 2-6.

 

Monoclonal Antibodies & Hybridoma Technology- Dr C R Meera

 

1. What are Polyclonal & Monoclonal antibodies?

Antibodies (Ab) are immunoglobulins produced against the antigen (An) by activated B -Lymphocytes. On activation, B cells differentiate into plasma cells and memory cells. Plasma cells proliferate to form clone of cells and produce large number of antibodies targeted against the antigen that had stimulated the entire process. However, Ans have multiple antigenic determinants or epitopes. Hence, on encountering an An, multiple clones of B cells are generated which will result in the production of antisera containing Abs or Igs of different classes with specificities against different epitopes of the same An. Such Abs are called “Polyclonal Abs”.

Abs produced by clones of a single B lymphocytes and directed against single antigenic determinant or epitopes are called “Monoclonal Abs”. Means, these Abs will bind with single specific epitope on an An. Ie; they are identical Abs with same specificity. Polyclonal Abs are heterogenous population of Igs whereas Monoclonal Abs are population of single type of Ab. Monoclonal Abs are useful tools for diagnostic and research techniques. The technique used for the production of large amount of monoclonal Abs is called Hybridoma technology.

2. What is Hybridoma technology?

Hybridoma technology is a versatile and efficient method for large scale production of monoclonal antibodies against desired antigen. Hybridomas- are somatic cell hybrids produced by fusing Ab producing B lymphocytes from spleen cells and Myeloma cells. Production of desired monoclonal Abs from these hybridoma cells is called hybridoma technology. This method was developed by Georges J F Kohler and Cesar Milstein in 1975 and jointly awarded Nobel prize in Physiology & Medicine in 1984 for this work.

Step 1- Immunization of laboratory animal

Lab animal like Swiss albino mice is immunized with the An against which we have to produce Abs. This An will be having multiple epitopes on it. B lymphocytes get activated against the epitopes of the An. After few weeks, the mice is sacrificed and spleen is removed aseptically.  Spleen is the secondary lymphoid organ and we can easily harvest B lymphocytes from spleen. Spleen is subjected to mechanical and enzymatic disruption followed by density gradient centrifugation to separate activated B cells from normal B cells of spleen. Now we have B cells capable of producing Abs against the multiple epitopes of the injected An.

Step 2- Fusion of cells to produce Hybridomas

B cells have only short life span in cell culture. Hence, to increase their life span in laboratory conditions they are fused with Myeloma (Blood cancer) cells. Myeloma cells used here are mutated Myeloma cells. Myeloma cells are cancerous B cells (Plasma cells) that can divide indefinitely in culture media. Their 2 genes are mutated. One is HGPRT (Hypoxanthine phosphoribosyl transferase) gene. Hence, they are not able to synthesize nucleotides by the Salvage pathway. Second mutated gene is Ig gene. As a result of this mutation myeloma cells could not synthesize their own Abs.  These mutations are represented as HGPRT^- & Ig^-.

Activated B cells and Myeloma cells are fused in the presence of chemical fusogen Polyethylene Glycol (PEG).  As a result of cell fusion, 5 types of cells are obtained.

• ·      Unfused B cells
• ·      Fused B cells
• ·      Unfused myeloma cells
• ·      Fused myeloma cells
• ·      Hybrid cells (Hybridomas)

Hybridomas are formed by the fusion of B cells and myeloma cells. Hybridomas will be of different types depending on the type of B cell fused with myeloma cells. Next task is the selection of this hybridomas from mixture of above cells. 

Step 3- Selection of Hybridomas using HAT medium

H= Hypoxanthine

A= Aminopterin

T= Thymidine

HAT medium is a selection medium for mammalian cell cultures. During cell multiplication, nucleic acid synthesis takes place in 2 pathways. The De novo pathway & Salvage pathway. Aminopterin in HAT medium blocks the De novo pathway. Hence the only the cells that can synthesize their nucleic acid using Salvage pathway can survive in HAT medium. H & T are major metabolites in Salvage pathway and HGPRT is the key enzyme. So HGPRT^- cells die in HAT medium.

Once the hybridoma mixture is added to the HAT medium, fused and unfused B cells die out in few days as they have short life span in culture media. They can not divide indefinitely in cell cultures. Fused and unfused myeloma cells will also die as they are HGPRT^- and Aminopterin blocks De novo pathway in HAT medium. Hybrid cells survive in HAT medium as they are HGPRT⁺ due to the activated B cell and divide indefinitely, property due to the myeloma cell. Hence, what will be remaining in HAT medium will be hybrid cells that are able to produce Abs against the different epitopes of the particular An. Now these hybridomas are mixture of B cells producing Abs of different specificities. Now our aim is to select and propagate hybrid cells that produce single type of Ab. So, we have to separate these hybridomas and grow them individually. So next step is isolation of hybridomas of single specificity.

Step 4 - Isolation of Hybridomas of single specificity

Isolation of hybridomas of single specificity is achieved by limiting dilution method. In this technique cells are distributed at very low density in multi well culture plates so that each well contain a single cell only.

 Step 5 – Screening of Abs produced

Next step is the screening of Abs produced by individual hybridoma cells in the multi well culture plates. Collected supernatants could be analyzed for Abs by techniques like ELISA and RIA.

Step 6 – Cloning & Propagation

Once the hybridomas producing the desired Abs are identified they are isolated, cloned and propagated. Now we have hybridomas producing Abs of single specificity or monoclonal Abs.

Step 7 – Characterization and storage

Finally, mAbs are characterized and stored, usually in liquid nitrogen. Now they can be readily used in treating and diagnosing diseases.  

3. Advantages & applications of Hybridoma technology

Discovery of hybridoma technology was a revolution in immunology.

• ·    Hybrid cells can be maintained indefinitely in cultures for the continuous production of mAbs in vitro.
• ·     Invivo maintenance can be done by injecting hybrid cells in the intraperitoneal cavity of mice and mAbs can be harvested from the ascitic fluid produced.
• ·      Hybrid cells can be kept frozen for prolonged usage.
• ·     Powerful tool of passive immunization.
• ·     Numerous therapeutic, diagnostic (bacterial, viral & other Ans) and research applications.
• ·mAbs against various Ans are now used in commercially available immunofluorescence & ELISA kits.