How does the publication cycle work?

What is the publication cycle?

The publication cycle is an inseparable and critical aspect that every researcher or writer needs to understand. This is because the publication cycle gives a tangible form to a theoretical concept, an idea, or an expression of writing talent. To use a commercial term, it is much like an assembly line where an idea passes through various inter-related processes and iterations before it develops into its final published form.

Content and medium: Two determinants of the publication cycle

The publication cycle differs based on two factors: the nature of content and the medium of publication. A writing output can belong to one of a myriad range of topics and publication mediums.  Some writers present their ideas in the form of research articles on various topics in, inter alia, journals, dissertations, conference papers, and scholarly books. Conversely, the output of other writers might be in the form of informal writings that appear in magazines catering to the general reader.

Apart from the nature of content, publications also differ in the medium selected for publication. Unlike most of the 20th century, publications are no longer limited to the print medium. In fact, the digital revolution and advent of the Internet have given an entirely new dimension to publishing with the popularity of articles and even books published on the web and in the electronic medium. Therefore, one needs to understand that the publication cycle, or the intervening processes for an idea to reach the reader, is determined by several factors. These factors determine the processes and the time cycle for a writing to be published in its final form.

Electronic publications include two categories. The first is the category of online publications on the World Wide Web. These include personal web pages of the author, individual blogs, online videos or presentations, as well as online research journals or periodicals. The second category includes electronic books, often referred to as e-books, which are bought and sold in the market, but the reader can access them only by using software on a digital device or a personal computer.

Conversely, the more conventional publications in print include research papers or reports published in journals, magazines, and books.

What does the publication cycle involve?

The publication cycle starts with the generation of an idea by the author or writer. This first step toward publication is basically an individualistic approach in the sense that it is a creative process and not a time-bound phenomenon.

After an idea takes root in the writer’s mind, the next step is to undertake the research that will help develop that idea into a well-constructed piece of writing. In this step, the authors search for existing literature on the relevant subject and identify the lacunae in such writing. This helps them make a useful contribution to their area of research.

The research work is followed by an informal communication among the authors (in case of multiple authors) that includes regular conversations on the phone and meetings for discussion of their research output. This stage provides a common platform for different authors to share ideas and views on a particular topic or idea of research.

The next major step involves report research. This could either be an informal approach adopted by the author or authors to share their research on their individual blogs or web pages, or a formal approach that includes white paper publications, report publications such as lab or research reports, and presentations at conferences and colloquia.

The next step is to report the findings as a publication in journals and/or magazines. Such publications provide a platform for popularization of the authors’ work, or to bring the research to the notice of a wider readership.

The culminating point of the publication cycle of a research idea occurs in a book or encyclopedia publication.  This is the most formalized medium of publishing a research work, and is recognized as the ultimate achievement for a researcher.

Each stage of the publication cycle is relevant because it constitutes a step in the ladder toward the final form of a research idea. Considered holistically, an understanding of the publication cycle facilitates the development of an efficient strategy for publication of a research work in an organized manner.

Conference papers vs journal publications: Which is the better publication route?

In course of their research, academicians often need to interact and exchange views with their colleagues to provide a firmer ground for their inferences. Such meetings help them debate their research topic with other like-minded participants and then assimilate the information that is presented through audio-visual media to produce a more conclusive finding. Therefore, seminars and colloquia are an essential part in the growth of any research. Often the proceedings of such meetings are recorded in the form of a collection of papers that were presented during the event.

On the other hand, a journal publishes research work, either on the web or as printed copies, after a rigorous process of review and a long approval cycle. However, once published in a reputed journal, your paper has an audience that you would otherwise have never had access to.

Why opt for conferences?

Conference proceedings have several advantages for a researcher. This is because conferences:

– Give a platform for interaction among research scholars who share a common interest.

– Have a faster review process and generate a faster feedback.

– Are often characterized by short presentations, so they manage to present the aim of the research clearly without consuming too much time.

– Include discussions sessions, which encourages exchange of views and ideas on the presentations.

– Allow interaction of scholars from all over the world who are engaged in the same or allied research fields.

– Have a predictable and time-bound review time.

– Help the presentations to be properly archived for reference in similar events held elsewhere on related research topics.

– Involve sponsors, who allure researchers with publishing credits and personal and professional benefits for attending the conference.

– Have high visibility and often leave a greater impact on the academic fraternity.

– Mainly focus on recent researches or up-to-date academic endeavors, unlike a journal that often takes a long time to finally publish a research.

Demerits of a conference publication

On the flip side, conferences have the following drawbacks:

– The review process is often superficial or cursory, i.e., there is no second round of reviewing.

– They have a low acceptance rate.

– The feedback from the research fraternity may be lukewarm compared to a publication in a journal.

– Economies of scale work against good quality publications because the publication is one of many expense heads for the organizers. Therefore, the production quality often leaves much to be desired.

Why opt for a journal publication?

A publication in a reputed journal presents the following advantages for the researcher:

– Research papers that are published in journals are thoroughly peer reviewed, including multiple review phases.

– The quality of research published in a journal is of a high standard.

– Journal publications carry deep analysis of a research work.

– Useful feedback is received from the reviewers, which help bring about substantive changes in the paper to improve the research analysis.

– Word and page limits are longer in the case of journals. This gives more scope to the researcher to express his or her thoughts and interpretations.

– A journal gives a chance to authors to revise their work based on the feedback and then re-submit it for further review and publication.

– Conference papers are never considered the ultimate in publishing a research. Often, conference papers can be converted to journal papers and published in reputed journals with a high impact factor.

Demerits of journal publications

There are also few demerits of journal publications. These include:

– The publication process is time-consuming.

– Due to such delays, the research topic might get outdated.

– Selection of journals is a difficult task. Sometimes, a good research is published in a sub-standard journal.

Both these routes to publication have their pros and cons. It must also be noted that conference proceedings and journal publications are not mutually exclusive; a situation may arise where one form of a research work might be published in the conference proceedings and another, perhaps more developed, form might be published in a journal. Therefore, for a more diverse and in-depth research output, both conference proceedings and journal publications need to play a significant part.

Importance of Statistical Review of manuscripts

Statistics: It is a branch of mathematics that deals with the collection of data, its analysis, interpretation, presentation and sequential organization. In simple terms, it deals with philosophy, logic, and expression of data.

Who does the statistical review?

Statistical review is basically done by the expert statisticians or authors and journal editors with statistical knowledge. It comprises of statistical and even methodological questions that are to be answered by the author or even the journal editors that are put forward by the reviewer.

Role of the statistical reviewers:

  • The statistical reviewers find out the possible statistical error sources in the manuscript, in turn increasing the statistical accuracy of the paper as well as ensuring quicker publication of the manuscript.
  • All forms of statistical data checking is performed by the statistical reviewers like checking the missing data, checking whether correct statistical methods were followed or not, checking whether the statistical methods were used appropriately or not, checking for statistical errors like error in level of significance during analysis of the data, checking whether appropriate name of the statistical package is mentioned or not along with the version used, checking whether the measurable units are properly mentioned or not, checking whether the tables and figures displayed in the manuscript hold a proper self-explanatory footnote or not, and so on.
  • They ensure proper statistical presentation of data throughout the manuscript; proper use of statistical language is also ensured by the reviewer in the data presentation section.
  • The reviewer also checks whether the conclusion section in the manuscript is justified or not with regard to the presented data.
  • They also cross check the feasibility of the discussion section based on the results.

Significance of statistical review:

  • If there is any kind of major statistical errors found in the data presentation section, then it may lead to the rejection of the research paper. So, reviewing of the statistical data and its proper presentation is of utmost importance for the author. The frequent statistical problems in the manuscript are found in data interpretation and presentation, its analysis and the study design.
  • Sound statistics is the foundation to high-quality research work interpreting quantitative studies.

Is self-plagiarism ethical?

Research papers or journals are the medium of spreading knowledge and new ideas evolved. Innovative and original piece of work would certainly be more educative and admirable. Nevertheless, authors and writers are often found to be reusing their old piece of work or some extracts from their previous published papers while writing a new research paper.

When questions are raised against this content reuse, authors claim that those stuffs are their own works and materials, and thus, they can reuse them as they wish, and it cannot be termed as plagiarism since they have not stolen the ideas from any other author or source.

The ethics of plagiarism are not applicable to such reuse, as a result of which it has been overlooked till date. While the discussion is whether this reuse is ethical or not, the publications and the journals, on the other hand, have set certain guidelines for such works citing it as Self-plagiarism.

What is self-plagiarism?

Self-plagiarism is a form of plagiarism where the writer reuses his/her own previously published work in portions or entirely while creating a new study paper. It can breach the publisher’s copyright on those published work when it is reused in the new study papers without appropriate citations. Let us now know more about the ethical aspects of self-plagiarism.

Self-plagiarism can be detected when:

a)  A published paper is used to republish elsewhere without the consent of the co-authors and the publisher of the paper or work.

b)  A paper of a large study is published in small sections with an intention to increase the number of publications.

c)  A previously written work either published or not is reused again in portions in the new study papers.

Although the laws of self-plagiarism are not enforced, it somehow reflects the dishonesty of the author. Moreover, the journals and the publishers are rejecting such copy-paste works as they are seeking writings based on original research findings and proper citations of all the references.

Nowadays, journals are also pointing out questions on the reuse of one’s own work. In order to avoid self-plagiarism, one should try to keep his/her work original, and in case it is necessary to include any portion from his/her previous works, it should be then properly cited with proper references. I hope this article will surely help you in detecting prospective self-plagiarism before submitting your paper or work to publications or journals.

BioConference Live 2014

President Barack Obama's participation in BioconferenceLive 2014 alongside ManuscripteditThe BioConference Live virtual neuroscience conference conducted on March 19-20, 2014, was an online event set to unite the neuroscience community via live video webcasts and real-time networking. Manuscriptedit participated in this high profile conference that saw the participation of President Barack Obama as well.

Researchers, post docs, lab directors, and other medical professionals learnt about recent investments and the scientific foci of the BRAIN Initiative through a panel discussion with key leaders from diverse scientific and funding regulatory agencies. The BRAIN Initiative was part of a new Presidential focus intended at reforming our understanding of the human brain.

The Neuroscience conference included topics from science journals like Behavioral and Cognitive Neuroscience, Epigenetic Regulation, Genetics of Neurologic Diseases, Molecular Mechanism, Neurologic Dysfunction from Human Diseases, and Nervous System Development. It also covered neurological diseases from lab to clinic, including Alzheimer’s, ALS, Epilepsy, Huntington’s disease, Multiple Sclerosis, Parkinson’s, traumatic brain and spinal cord injury, and neuropsychiatric disorders.

In addition to topics on diseases, the conference also covered emerging therapies, like combinatorial therapies, immunomodulation, myelin repair, non-coding RNA, neurorobotics, neuroengineering, stem cells, and imaging technologies – in vitro and in vivo.

The intense two-day conference covered original research data, teaching presentations, broad overview of new frontiers given by thought leaders in the field and discussion forums. Attendees learnt new concepts, tools and techniques that they can apply to research and diagnosis.

Size does matter: Nano vs. Macroscopic world

We live in an era of nanomaterials, nanotechnology, and nanoscience. What is so special about this nano world? How different is it from the macroscopic world of conventional bulk materials? How size influences the difference in properties in these two distinct worlds, although the basic material is same? For example, the properties of gold nanoparticles are distinctly different from the bulk gold. One simple answer is nanoparticles consist of fewer atoms to few thousand atoms while the bulk materials generally Fig 1 gold macro vs nano composed of billions of atoms. Look at the image below. At nanoscale, gold does not look even yellow! All of us know that gold (in bulk) is an inert metal. However, the same metal at nanosize of about 5 nm works as a catalyst in oxidizing carbon monoxide (CO). Therefore, size does influence the property. But, how? What happens when a material breaks down to nanoscale? Part of the answer lies in the number of surface atoms. Let’s elaborate it. We know that at bulk state gold forms face centered cubic (fcc) lattice where each gold atom remains surrounded by 12 gold atoms, even the gold atoms at surface is surrounded by six adjacent atoms. In a gold nanoparticle, a higher number of atoms sit at the surface, and surface atoms are always more reactive. These large numbers of exposed atoms in gold nanoparticles compared to the bulk material enable gold nanoparticles to function as a catalyst.

Now what happens to the color? At nanoscale, gold loses its vibrant yellow color. While light gets reflected from the surface of the gold at bulk state, the electron clouds resonates with certain wavelength of light at nanoscale. Depending on the size of the nanoparticle, it absorbs light of certain wavelength and emits light at different wavelength. For example, nanoparticles of sizes about 90 nm absorb red to yellow light and emit blue-green, whereas particles around 30 nm in size absorb blue and green light and appear red in color.

The physical properties such as melting point, boiling point, conductivity, etc. also change in nanoscale. For example, Fig 2a when gold melts in its bulk state regardless whether it’s a small ring or big gold bar, all melts at the same temperature. But this is not true for nanoparticles; with decrease in size, the melting point lowers and it varies by hundreds of degrees (Check the inset picture). This is because when a matter reaches nano-regime, it no longer follows Newtonian or classical physics, rather it obeys the rules of quantum mechanics. The nanoeffects which are relevant for nanomaterials are as follows: (i) Gravitational force no longer controls the behavior due to the very small mass of the nanoparticles, rather electromagnetic field determines the behavior of the atoms and molecules; (ii) Wave-particle duality applicable for such small masses, where wave nature shows pronounced effect; (iii) As a result of wave-particle duality, a particle (electron) can penetrate through an energy region or barrier (i.e. energy potential) which is classically forbidden and this is known as quantum tunneling. In classical physics, a particle can jump a barrier only when it has energy more than the barrier; Fig 2_tunneling therefore, the probability of finding the particle on the other side the barrier is nil if the particle possesses less energy than the barrier. On the other hand, in quantum physics, the probability of finding a particle, with less energy required to jump the barrier, on the other side is finite. However, to have a tunneling effect, the thickness of the barrier should be comparable with the wavelength of the particle and this is only possible in nanoscale level. Based on quantum tunneling, scanning tunneling microscope (STM) is created to characterize the nanosurfaces.

(iv) Quantum confinement i.e. electrons are not freely movable in bulk material rather these are confined in space. Size tunable electronic properties of nanoparticles arise due to quantum confinement.

(v) Energy quantization i.e. energy is quantized. An electron can exist only at discreet energy levels. Quantum dots, a special class of nanoparticles of size 1-30 nm, show the effect of energy quantization.

(vi) Random molecular motion: At absolute zero molecules are always moving owing to their kinetic energy, although this motion is not comparable to the object at macroscale. However, at nanoscale, this motion becomes comparable to the size of the particle; hence, influence the behavior of the particle.

(vii) Increased surface-to-volume ratio: The changes in the bulk properties (mp, bp, hardness, etc.) can be attributed to the enhanced surface-to-volume ratio of nanoparticles.

Therefore, in a nut shell, because of the above mentioned changes, the properties of a material in nanoregime differ from macroscale.

Interdisciplinary research – Direct Imaging of Single Molecule

Interdisciplinary research has immense potential. I have talked about one of the major discoveries of modern science based on interdisciplinary research in my previous blog, posted on 29th July 2013 (http://blog.manuscriptedit.com/2013/07/ interdisciplinary-research-nobel-prize-chemistry-won-biologists/). Today, let us take another example, where one chemist and one physicist came together and presented us with the direct image of internal covalent bond structure of a single molecule using one of the advanced imaging tools, non-contact Atomic force microscope (nc-AFM). Image1Dr. Felix R.Fischer (http://www.cchem.berkeley.edu/frfgrp/), a young Assistant Professor of Chemistry at University of California (UC), Berkeley along with his collaborator Dr. Michael Crommie (http://www.physics.berkeley.edu/research/crommie/home), also a UC Berkeley Professor of Physics captured the images of internal bond structure of oligo (phenylene-1, 2 ethynylenes) [Reactant1] when it undergoes cyclization to give different cyclic compounds (one of which is shown in the inset picture http://newscenter.berkeley.edu/2013/05/30/scientists-capture-first-images-of-molecules-before-and-after-reaction/). Chemists generally determine structure of molecules using different spectroscopic techniques (NMR, IR, Uv-vis, etc.) in an indirect manner. The molecular structures, we generally see in the textbooks result from the indirect way of structure determination, either theoretical or experimental or both. It is more like putting together various parts to solve a puzzle. But now, with this ground breaking work of two scientists from UC Berkeley, one can directly see for the very first time in the history of science, how a single molecule undergoes transformation in a chemical reaction, how the atoms reorganized themselves at a certain condition to produce another molecule. No more solving puzzle for next generation of chemists to determine the molecular structure.

HOW interdisciplinary research made it possible:

Well, it was not easy task for the scientists to come up with these spectacular molecular images. Imaging techniques such as scanning tunneling microscopy (STM), tunneling electron microscopy (TEM), have their limitations, and are often destructive to the organic molecular structure. Advanced technique like nc-AFM where a single carbon monoxide molecule sits on the tip (probe) helps in enhancing the spatial resolution of the microscope, and this method is also non-destructive. The thermal cyclization of the Reactant 1 was probed on an atomically cleaned silver surface, Ag(001) under ultra-high vacuum at single molecular level by STM and nc-AFM. Before probing, the reaction surface and the molecules were chilled at liquid helium temperature, 40K (-2700C). Then the researchers first located the surface molecules by STM and then performed further finetuning with nc-AFM, and the result is what we see in the inset picture. For cyclization, the Reactant 1 was heated at 900C, the products were chilled and probed.  Chilling after heating did not alter the structure of the products. The mechanism of thermal cyclization was also clearly understood, and the mechanistic pathway was in agreement with the theoretical calculations. From the blurred images of STM, Dr. Fischer and Dr. Crommie along with their coworkers presented us crystal clear molecular images with visible internal bond structure. This ground breaking work shows the potential of nc-AFM and unveils secrets of surface bound chemical reactions which will definitely have a huge impact on oil and chemical industries where heterogeneous catalysis is widely used. This technique will also help in creating customized nanostructure for use in electronic devices.

Again this path breaking work was possible due to the collaborative research between chemists and physicists. Hence, the interdisciplinary researches have endless potential.

References

1.    de Oteyza DG, Gorman P, Chen Y-C, Wickenburg S, Riss A, Mowbray DJ, Etkin G, Pedramrazi Z, Tsai H-Z, Rubio A, Crommie MF, Fischer FR. Direct Imaging of Covalent bond structure in Single-molecule chemical reactions. Science (2013); 340: 1434-1437

 

Interdisciplinary research – Nobel Prize for Chemistry was awarded to two Biologists

Modern scientific research does not confine itself to any restricted boundary.  Nowadays, it is all about interdisciplinary research. In 2012, Nobel Prize for Chemistry (http://www.nobelprize.org/nobel_prizes/chemistry/)was awarded to two eminent biologists, Prof. Robert J Lefkowitz and Prof. Brian Kobika, for their crucial contribution in unveiling the signalling mechanism of G protein-coupled receptors (GPCRs). It’s a lifetime work of both the scientists. Dr. Lefkowitz, an investigator at Howard Hughes Medical Institute (HHMI) at Duke University, is also James B Duke Professor of Medicine and of Biochemistry at Duke University Medical Center, Durham, NC, USA. Dr. Kobika, earlier a postdoctoral fellow in Dr. Lefkowitz’s laboratory, is currently Professor of Molecular and Cellular Physiology at Stanford University, School of Medicine, Stanford, CA, USA.

Transmembrane signalling of one GPCR “caught in action” by X-ray crystallography

GTP (guanosine triphosphate) binding proteins (G-protein) act as molecular switches in transmitting signals from different stimuli outside the cell to inside the cell. However, for doing this G-protein needs to be activated, and that is where GPCRs play the most important role. They sit in the cell membranes throughout the body. GPCRs, also known as seven transmembrane (pass through the cell membrane seven times) domain proteins, detect the external signals like odor, light, flavor as well as the signals within the body such as hormones, neurotransmitter.1 Once the GPCRs detect a signal, the signal is transduced in certain pathway and finally activate the G-protein. In response, the activated G-protein triggers different cellular processes. Binding of a signalling molecule or ligand to the GPCR causes conformational changes in the GPCR structure. As a result of extensive research of 20 long years, Dr. Lefkowitz and Dr. Kobika not only identified 800 members of GPCRs family in human but also caught in action how these receptor proteins actually carry out the signal transduction with the help of high resolution X-ray crystallography. The crystal structure of ß2-adrenergic receptor (ß2AR), a member of the human GPCRs family was reported by Dr. Kobika and his colleagues in 2007.2 The hormones adrenaline and noradrenaline are known to activate ß2AR, and the activated ß2AR triggers different biochemical processes which help in speeding up the heart and opening airways as body’s fight response. The ß2AR is a key ingredient in anti-asthma drugs. One of the major breakthroughs came in 2011 when Dr. Kobika and his co-workers unveiled for the first time the exact moment of the transmembrane signalling by a GPCR. They reported the crystal structure of “the active state ternary complex composed of agonist-occupied monomeric ß2AR and nucleotide-free Gs heterotrimer”.3 A major conformational change in ß2AR during signal transduction was discovered.

Now what is so special about GPCRs? Well, these proteins belong to one of the largest families of  all human proteins. GPCRs are involved in most of the physiological activities, and hence are  the targets of a number of drugs. Determination of the molecular structures of this class of receptors not only helps the researchers to understand the actual mechanism of different cellular processes but also help them to design life saving and more effective drugs. So, in a nut shell, this scientific breakthrough was possible due to the involvement of experts of different areas of science such as, chemistry, biochemistry, molecular and cellular biology, structural biology, cardiology, crystallography.

 

References

 

  1. Lefkowitz, R. J. Seven transmembrane receptors: something old, something new. Acta Physiol. (Oxf.) 190, 9–19 (2007).
  2. Rasmussen, S. G. et al. Crystal structure of the human b2 adrenergic G-protein coupled receptor. Nature 450, 383–387 (2007).
  3. Rasmussen, S. G. et al.  Crystal structure of the b2 adrenergic receptor–Gs protein complex. Nature 477,  549-557 (2011)